I currently have 62 entities and around 11 year long save, after several researches (or perhaps it is tied to time?), research gained from study goes all the way down to one point per study, essentially stagnating research. The issue resolves itself for some time after reloading save, but it comes back soon enough. Could it be some calculation error?

There isn't anything regarding that in the log, but just in case you need it anyway:
https://gist.github.com/HugsLibRecordKeeper/234d672bd8c5d54901cb99db6c6c98fd

Edit: After more observation, it seems to be related to having multiple active maps (be it a caravan event or some dungeon map (obelisk backrooms, pit gate etc.). I assume it takes one of these maps as it's entity value research calculation map and doesn't reset even after these maps are closed, only resetting on save reload.