Well if it is only the file name, I am using 123renamer, to do mass renameing, it has a replace/remove option, so hopefully its only the filename that hangs the database, otherwise alot more work will be involved.
I would have thought it was one or the other, ie: if the file has the ID3 tAG then xlobby refers to that, if no tag then the filename perhaps.
I recall having to look at this quite some time ago and I think all I did was change the TAG not the file name. My audio files are APE so I was able to right click the file and change the relevant TAG details... once I knew where the errors were.