I've had similar issues a number of times. At first, I thought it might be a long filename or some incompatible character in the path or name -- but it wasn't.
All I needed to do was change the name ever so slightly by adding or subtracting a single character, and then, voila! File is recognized and added upon auto import. Really, how do you explain that?
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I notice odd quirks here and there do pop up like some missing/broken files/paths not being automatically removed, even though my settings were to remove broken links. Most of them do get updated or removed, but not all -- so I find myself every now and then manually having to remove files from the library.
I suspect the best solution might be to clear my library and re-import everything every year or so... Then, again, all those hundreds of particles stacks I created (some of which I did not even create myself, but just seem to be particles stacks from other files reappriated to other files -- dunno how that even happened) eh. I have a feeling that might break things even more sooo... ugh. Maybe just not? But I'm trying to avoid that option for now.