DFHack has rolled out a new Notify utility that reports when Nemesis Records are missing and they recommended sending the save file to you for review. I have not noticed any direct problems with saving or loading or crashing of any sort yet. I am sending this along for investigation regarding possible save file corruption (sounds scary). The following active units are reported to be missing their nemesis records:

Bim Besmarzuntir, Elite Marksdwarf
Mebzuth Litastkirar, Elite Wrestler
Tekkud Adeklogem, Bard
Sazir Avuzdural, Fishery Worker
Dumat Shetbethber, Bard

The only mod that I've used is DFHack. I (ab)use the "cleanowned scattered nodump" and "gui/autobutcher" commands regularly, as well as some of the other background automations that it provides for kitchen food use and such.

Thanks for checking this out! Also, take a peek at my cool lava-breathing serpent structure on the surface if you have a spare moment. It turned out better than I expected and I still have some plans to expand more artillery on the top level if I keep this world running.