The tl;dr version is there's
(1) the obvious epistemological point that we haven't discovered everything about the past
(2) a significant amount of evidence pointing towards multiple cases of a culture being more "advanced" than generally recognized by the mainstream (historically happened a lot due to racism)
(3) a deeply elitist culture among academics, which leads to a wide variety of problems
(4) an institutional "ghettoization" of challenges to mainstream theories (I personally remember when people who thought a meteor killed the dinosaurs were still being called schizo religious cranks in textbooks)
(5) a resulting very low public trust in academia as an authority on matters of science as well as history (especially political things)
(6) a lot of kooky grifters eager to take advantage of a topic that generally lacks rigor but has more than enough evidence to make a compelling case and has a very catchy premise
Hancock specifically is definitely in the kook camp, being apparently motivated by an ayahuasca trip where he "met" members of his lost civilization and was tasked with telling the world about them. That said, he often does uncover real data and valid points. At the same time he also uncovers nonsense. This is a common situation with these people, and as outlined above, it has a lot to do with the way that science and academic literature is generally gatekept within capitalist society. It's important to note that none of these ideas essentially originated with Hancock. He simply collects them and tries to fit pieces together where a layman with a special interest can.
It's absolutely 100% guaranteed that people in the past had more technologies than they are given credit for, as a general thing, simply by the fact that the science can only say what it has evidence for. The most bleeding edge experimental stuff people had at any given time is also the least likely to survive into the archaeological record, since most of the archaeological record consists of things people threw away or abandoned. Any relatively sophisticated technology is valuable (if only because of the labor time invested in it) and is going to be prioritized as something to take with you when you leave a site. This is a very important point, but one that is often ignored. That's not to say this is a flaw with the science, but it is a limitation, and it does need to be acknowledged. We can't say with certainty that a people group did not have a certain (plausible) technology simply because we don't find direct remnants of it. For instance, we have drilled holes in stone, but none of the drills themselves were left behind. It's then open to argument what kind of technology the drills used. Would drills of X material have been sufficient? And what about tools that didn't leave evidence as durable as holes in stonework?
Another key point directly related to this is the fact that the farther back in time you go, the less survives. Especially in areas with dramatic climate change, like the retreat of the ice sheets in the northern hemisphere or the transformation of the Sahara from a tropical jungle into a desert 5-6000 years ago. https://en.wikipedia.org/wiki/African_humid_period Notably to the topic, this climate change is attested in ancient literature (including Herodotus), and is half the distance back in time as the "great flood" proposed by Hancock and company (sea level rising due to deglaciation at the end of the younger dryas, ~11,500 years ago). While a lot of these areas are known to support human habitation, not much survives or has been discovered, because whatever was left out in the open got either washed away in glacial melts or covered in desert sands. It creates a similar bias in the data that gave us the notion of "cavemen" being the norm - there were also people building houses contemporary with cavemen (we know this now), but living in caves makes your artifacts more likely to survive, because the caves protect them from the elements. We have the cave paintings, but we don't have paintings that were made on the bare rock outside. Basically there's a big blindspot on the topic.
There's also an ideological bias against catastrophism which has a long history across the sciences. This is mainly because The BibleTM and other religious texts give a lot of weight to catastrophes and cranks have long tried to legitimize these stories with science. Unfortunately, however, the reality is that catastrophes that disrupt life on Earth do occur, not not that rarely either. This is beyond doubt now, and the discovery of the Chicxulub crater (dinosaur meteor) off the Mexican coast is why. Astrophysicists tend to be pretty vocal about the danger of impacts and how we should take measures to ensure we can protect ourselves in the future. This unfortunately has not penetrated to the field of archaeology and history as much. One could argue this is due to it being a softer science and therefore having a fundamentally different culture. One could argue this is due to seeing that sort of thing as in incursion on their turf. Both I think are factors. The latter has a stronger case since you can see some archaeologists get mad at other scientific fields getting involved, like notably geologists (the dating of the Sphinx being a big one here). Catastrophism vs gradualism vs stability has been a (mostly philosophical) debate across the sciences though, so maybe archaeology is just late on getting with a program that reality is typically gradual change occasionally interrupted by major shake-ups.
As for the possibility of any specific ancient undiscovered "civilization" that really depends on the things you are attributing to them. There's certainly evidence that suggests some kind of major piece (more likely a few) missing from the puzzle. In terms of the "tech level" that's possible to have existed and then disappeared without being rediscovered yet, from what I know on the subject it could be pretty much anything pre-industrial revolution. If there were people burning fossil fuels for energy or especially had discovered things like plastic or nukes, we would not have missed the signs. But pretty much any "stage" before that, and the evidence might be there; we just haven't really looked for it. There are just too many assumptions about what happened, and looking for, say, medieval-Europe levels of metallurgy by examining heavy metal accumulation in ice cores *could* be done in theory but just isn't.
Of course, another really important point about technology is that real life is not a 4X game. There is not some pre-determined tech tree that people can follow. This is evident from just looking at IRL history. When you see people from different contemporary cultures meet each other, they often find each other having pretty distinct technologies. That's because technology is an adaptation to a specific need and context. While the discovery of a given property of physics, chemistry, etc is not going to differ much due to culture (other than things like opportunity), the application of that knowledge will vary a lot depending on what problems are being solved. So if we compare a pretty classic example of like the Spanish Conquistadors to the Meso- and South-American indigenous empires, we find a huge disparity not in "tech level" so much as in priority. The Spanish were comparatively well equipped for warfare thanks to the European social context making that a big priority. Meanwhile, the Aztecs had a highly sophisticated water management and irrigation system and complex city planning. The Inca had a huge road network and an advanced terrace farming system. We don't know what the Amazonian people had, but we keep finding the ruins of city complexes buried under the rainforest. The Americas in general seemed to have a greater priority on developing complex agricultural methods. Consider how many global staple crops are from the New World, a product of the cultivation technologies employed by indigenous Americans that went in a different direction from European styles of farming. All this is to say, I think it's mistaken to think too much in terms of "advancement" of peoples, when whatever technology a people group has will be highly specific to their situation. This complicates the issue in terms of knowing what physical evidence to even look for. It might be more useful to think about continuity, longevity, and overall scale.
One of the biggest drawbacks to the idea of some large *global* society in the ancient past is the lack of evidence for biological dispersal. This is true both for humans (lack of genetic evidence) and for other species (not seeing evidence for something like Columbian Exchange). There are some caveats here, though, in that domesticated species (plant or animal) appear to be able to go feral and return to a basically wild state very quickly. Rice is a good example here, with some (mainstream) theories about it being domesticated multiple times. It seems rice can feralize in as short as one generation, leaving little to indicate it was ever domesticated (other than perhaps re-domestication being easier). Feral hogs as a contemporary example in North America can feralize similarly quickly. Questions arise with the case of a domesticated species being moved to a new continent, though. How well could domesticated beans from North America survive if released into the wild around Mesopotamia for example? There's also the issue here of genetic absorption. Sometimes when populations interact, all genetic evidence of one is fully replaced by the other. This happened for instance with most if not all American dog breeds. Chihuahuas are an Aztec breed, but their genetic lineage has been completely overwritten by European dog ancestors. Something similar may have also happened with humans and other Homo species. So this is potentially a case of "absence of evidence is not evidence of absence."
And finally of course, in general you have a problem of academics not liking change. "Science advances one funeral at a time" and so on. The most illustrative case germane to this topic is easily the Clovis First controversy. Basically, the Clovis culture are the people everyone has heard of coming to the Americas over the Bering land bridge during the ice age ~13000 years ago. For a very long time it was accepted that the Clovis people were the first to reach the Americas. This has since been shown not to be the case by a variety of evidence. However, until quite recently (and even now in some circles) this new evidence (mainstream archaeology mind you) was viciously opposed because it challenged the established narrative. A lot of archaeologists could lose standing or have some of their work outmoded if such a major upset was allowed to happen. But reality has more or less caught up on that topic, with evidence like the White Sands footprints being now accepted by most (though still somewhat controversial).
https://en.wikipedia.org/wiki/White_Sands_fossil_footprints
All of this said, be careful what information you absorb on this topic. There are not only cranks but also outright white supremacists all over it (trying to prove hyperborea lol), but tbh that's not so different from mainstream archaeology and history. There are few decently skeptical people who try to approach things in a neutral/objective way without majorly sensationalizing things or being idiots. Most people involved are very firmly in one "camp" or the other and tend to come with their own host of biases. It's also ripe for ridiculous flame wars, and some people (usually academics) can be incredibly vindictive and personal about this stuff. Flint Dibble, who went on Joe Rogan's podcast to debate Hancock, and has started very publicly and dramatically beefing with a smalltime youtuber (DeDunking, one of the rare reasonable ones) who criticized his arguments in the debate. That beef is currently blowing up into a culture war type situation. And that's basically the extent of the "conspiracy" here: individuals with a personal stake in a specific (pre)historical narrative lashing out at questions that potentially undermine their career. It's way more sad and pathetic than Big Archaeology hiding Atlantis and El Dorado.
Last but not least, it must be said that nothing is as ironic as archaeologists calling anyone else racist, given what their field gets up to past and present.
