I would go ahead an log this in the official bugs thread, with a link back to this thread. Either you shouldn't be able to obsolete basic tech components, or you should be able to un-obsolete them.
Sneer, unless you have database access there is nothing you can do. This is one of those little known issues players are supposed to avoid. As you've found there is no in game mechanic to reverse setting basic tech items from hving been flagged as obsolete. The flag is at a race level, so it will not affect new games.
Okay, I'm going to assume that you are looking at the technology report and not the design tab. Go to the design page where you first obsoleted engineering bays(not the tech view). click the show obsolete checkbox. it should look something like the attached image. are engineering bays visible there? if they are click on them, and click obsolete again. If they are not then something is seriously wrong with your particular version of aurora and you should reinstall it.
Click on show obsolete tech on the design tab of the F5 ship design page. go to the obsolete tech you want to unobsolete, and click obsolete again. the switch is a toggle.