I've got this as well, I think. The more systems and planets I discover (or animals and plants, not sure what causes this) older animals, plants and checkpoints appear to be overridden or something?
E.G. Yesterday I browsed my list of discoveries, and went all the way to my starting planet. The system and all the planets I've ever been to are clearly marked as being discovered by me, the planets list 100% completion for animal scans but I can't see any animal or plant in the gallery and all of them appear as ???????.
I then checked every planet in the list until I hit one that was starting to be "corrupted". It only had 3 checkpoints (I usually hit up a lot more) and only 3/9 animals discovered (worst case scenario I end up with 2 animals undiscovered). I memorized the planet, and went on playing and discovering new stuff.
The next day, browsed the list again. The planet was wiped clean and so were a couple more. There's definitely something off. And it's not the offline thing.
EDIT: Just to be clear enough, discoveries are being erased in chronological order. First system, second system and so on. It's not random. It's a pattern, starting from your very first discoveries.