Maybe you've already narrowed it down by now, I haven't read all the recent posts. But my unqualified shot in the dark: Is it absolutely certain that it is the saving rather than the loading process that causes the error?
I began a new game with 4 distant starting NPRs briefly after 1. 8 release and kept manual db copies periodically. A slow setup, two encounters with Trappist aliens, and, I don't remember exactly, about 35, in any case less than 40 (now very quick, thanks to C# Aurora) game years later, I had an unrelated program in a buggy script debug mode crash while saving aurora, and I thought that might have caused a save corruption: Next time I started Aurora, all ground units were gone (in total maybe around 40, most of them on Earth, a handful on fledgling colonies, and possibly 1 or 2 in transit on commercial transports, plus several garrisons on CMC rocks). As for saving, Aurora had been running idle in the background for longer periods at times, so the save intervals were irregular. And it is possible that I saved twice without advancing time.
I have no experience with SQLite or C#, but I took a brief look into the db with an SQLite DB Browser, and it seemed that most if not all of the units were still basically listed in the formation table with their names, template numbers, etc. Yet Aurora couldn't load the ground units, everything else seemed to be fine. But as I had somewhat botched my desired setup (a gloomy pacifist Antarctic Union of WWIII survivors that came out way too militarized and also too populous), didn't suspect yet that this might be a general bug and feared there might be more serious, less obvious save corruption elsewhere, I decided to start over when the next version is out . . . and wiped the manual saves, so I cannot pass on the db in question.
But if it is just possible from other bug reports that the cause might be in the input rather than the output, it might be worth to glance over the startup/load/initialization function/s or whatever it is that gets the data into the running program. In case it's relevant: I had deleted the "Federated Nations" (? or something like that) example/default game after my own Antarctica setup.
Although I've been drawn into a descending orbit around Aurora for years and browse the forums periodically, I just registered now. So, with my first post: Many thanks for sharing a marvelous game with us and your continued efforts to make us spend many more hours with it. And to the generally helpful community here for answering all of my Aurora 4x questions so far, before I had ever asked them.