The reason that I was trying to delete the old game was that I just ran into the same "can't find research projects that should be there" problem that someone else reported a while back.
I'm about 7 years into a conventional start game, and I realized I couldn't see projects like the next research or construction level anywhere (neither current, nor queued, nor available). Finally, I started cancelling researchers' projects 1-by-1, and discovered that the missing projects reappeared as projects were deleted.
[long pause while poking around in DB]
Ok - I'm pretty sure I know what's going on. I've got a researcher "Eve Richards" who's working on 12cm lasers. When I cancel the project, Fuel Production 24,000 magically reappears. Here's the interesting fact: Eve Richards' project ID (which is the key for the ResearchProject table) is #669. The TechSystemID (key in the TechSystem table) for Fuel Prod 24,000 is #669. Hmmmm seems like a coincidence :-) It looks like the query that displays the available research projects is somehow confusing the project ID with the TechSystemID.
John
PS - Any chance of getting a 5.41 patch for this one and the officer auto-assign bug? On the auto-assign, I don't need a DB repair, I'd just like Aurora to "go forth and sin no more" :-)