Items wrongly located in Trash

OK, this one’s kind of scary. I noticed a few months ago that a lot of files that I definitely need and do not want to delete come up in the Trash when I search for them. I just figured that I’d accidentally put them there as part of something I must have done to a large number of files, and resolved basically never to empty the Trash (there are over 1700 items in it, so it would be tedious to go through them all one by one).

Just now, though, I figured out that something way worse was happening. I found an entire group (incidentally, a very important one to my dissertation) that thinks it’s in the Trash (i.e. searches find it in the Trash and nowhere else, and Info tells me it’s in the Trash), even though I can see clearly that it’s in the regular folder hierarchy. At least some of the folders in the same parent folder have no such problem. The problem folder and most of the files inside it are not replicants.

Any solutions to this somewhat scary bug?