I am resurrecting this (kinda) old thread.
I recently did a reorganisation of my PDF files and folder structure. What this means is that I moved them to other places, did some reshuffling, etc. but all PDF filenames remained the same.
I also tried to clean up the database (as suggested above by @koppor) and to make PDF paths relative. Unfortunately, this did not make PDF paths relative as I can see that they are still fixed as they were.
EDIT: I also just discovered and tried the Automatically set file links option in the Quality menu, to no avail. Mind that in Library → Library properties the General file directory is set to “.” i.e. the directory where the .bib file is located. But JabRef still cannot find the files anyway. It just searches for the files and then says: Finished automatically setting file links. No files found.
What I need to do, actually, is to reconnect all the entries in my .bib database to the original PDF files that were shuffled around. Is this possible at all? Can JabRef rediscover them automatically by filename i.e. author - title [year].pdf?