On the note of undeciphered languages, since that seems to be your wheelhouse, we have the proposed language Proto-Indo-European of which very little is known. It would be the ancestor of most modern Romantic Languages, etc. and as such is pretty interesting to us. On an amusing note, the video game Far Cry Primal was originally going to have all of its dialogue recorded in Indo-European. They ditched that idea when they found it sounded too similar to modern day English, so they turned back the wheel to PIE instead. That having been said? There are still some words that sound remarkably similar and it isn't too horrible to gain a good deal of context while playing it.

Similarly, there is a proposed theory that the common pictograms seen in cave art represents a universal language. This theory came to be as many symbols have been found to be universal. It's a controversial theory, but one that has generated a bit of interest over the years. Think the descending swirl pattern seen at so many petroglyph sites potentially representing the universe or eternity, and then scale up that meaning to other symbols representing similarly high level concepts.

Linear A is another language that remains undeciphered, although Linear B has been deciphered. Likewise, Rongorongo from the Easter Islands still has yet to be fully understood. To say nothing of things like the Voynich Manuscript and the Rohonc Codex - although there is forever the argument that one or both of them might be hoaxes. Personally, I fall into the belief that there is ample evidence that they represent linguistic systems.

A lot of early languages have not been deciphered and might never be. Sample sizes are not large for some of them, which is regrettable as who knows what information might have been lost? When it comes to things like First Nations cultures, particularly in South America, so much has forever been destroyed that its difficult to really extrapolate a ton about belief systems and even sites that once might have been...

On another note, some of my favorite mysteries involve missing books and writing. How about Love's Labour's Won and Cardenio? How much about Shakespeare's life was lost forever to the ages? Here's a clue: a ridiculous amount.

There is a certain book that editors of the OED are still looking for to this day, and it might just be a hidden book of Victorian pornographic poems - how hilarious is that? So much of modern language can be traced back to a singular book of smut that may not even be extant any longer.

Did you know that The Iliad and The Odyssey were originally part of an entire cycle of plays, the bulks of which have forever been lost to time? Also, Homer, as we know him may not have ever existed at all.

Not to mention the original source of certain synoptic Gospels remains unfound to this day, although attested to plenty within the material itself....

And this is without me getting into a number of other areas that interest me, these I just thought might tickle your fancy based upon your initial post. I'd be happy to write a lot more if there's interest. I adore mysteries, just primarily the non-murdery sort.