Minecraft – How to ensure that ‘gamerule keepInventory true’ is persistent across server restarts

One possible reason could be data corruption. The Random Seed of each map is saved in the file, and this seed determines how the world looks. Due to data corruption during the crashes it could be that this seed has changed, which would effectively screw everything (but would deliver interesting results for sure).

Another possible explanation is that you either got a completely new map¹ or chunks got corrupted/replaced/lost.

Anyway, my best advice is to restore from backup. Even if you change the seed back (given that you know the original one) or find the corrupted chunks, there's not much to gain. Parts of the world are already corrupted and you could only remove them and let them regenerate.

¹: Don't laugh, that happened to me once...took me ten minutes to figure that out.

Yes, the Nether is generated the same way as other terrain (in fact it's just a special biome). It uses your world seed to generate it, so re-generating will not affect the layout of it (although there may be slight changes, such as the position of mushrooms, but I'm guessing that this doesn't bother you too much).