Files disappeared from library, "missing" files not really missing

I had a folder with 3 files in different formats for each image.  These were imported several days ago, grouped into stacks, captioned, tagged, etc. and synced to the files.  They continued to exist in the library some time afterward, but today when I opened lightroom all of the jpg versions of all of the images and all 3 formats of one image in particular had vanished from the library.  It did not claim that it could not find them on disk (and in fact the files *do* still exist on disk right where they should), they just didn't show up.  I was able to re-import all of the jpg images without trouble, but for the other two formats of the one missing image, importing one of them fails because it "already exists in the library," and the other one is willing to import but then doesn't show up in the folder or the recently imported files list.  When I try to synchronize the folder, it suggests that I import that file, but it never actually does.  Since importing the jpgs, it also suggests that I remove 53 "missing" files, the number of jpgs imported.  When I view the missing files in the library, it shows only 2 of the jpgs, one of which belongs with the files that will not import and neither of which is actually missing--they can both be synchronized just fine by clicking the little synchronize icon on the actual photo.
Does anyone know what's going on here and how I might be able to get the files that won't import back into the library?  And how to be sure that files won't just go away on their own again?
Edit: to be clear, missing versions of files were definitely not stacked with the other ones and the "don't import duplicates" box was not checked when re-importing the ones that won't re-import

I managed to get the photos that wouldn't import back in by deleting them directly out of the database and then reimporting them into lightroom. I'm a little concerned that they disappeared in the library view in the first place, though.  Does this sort of thing happen often, and under what circumstances?  I'm still in the free trial period and was very close to buying the program, but now I'm not so sure.  If I'm using an application to manage my photos, I want to know that it's actually managing all of the photos I put into it and not randomly forgetting about them.
I'm still having the not-really-missing files problem, though.  I think it may actually be because they got associated as "sidecar" files somehow and are now in there twice, once as the sidecar file and another time as a separate jpg image.  I'm not really sure why only one of them shows up in the missing images view, I think it might be because I edited that one so it's in a slightly different state from the others?  If there are any tips on how to resolve that state, I'm all ears, I'd like it to stop telling me I have 53 missing files when I don't.

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