Now all my pdfs are Question Marks and don't open from bibdesk.
I'm happy for a fix in perl, ruby, python, whatever is quick.
How and whether you can fix this depends on what you have done in the mean time with the .bib file, whether you saved compromised data. So I cannot say in general how to do that.
You should realise that BibDesk keeps three pieces of data for linked file: a relative path, an absolute path, and a file identifier. The problem is that for you the file identifier is basically useless, because you use an external volume, and moreover, you changed that, so the identifiers were changed. You definitely changed the absolute paths. And I suspect you also changed the relative paths. So any link to the files was broken. (I am quite frankly still a bit surprised when users expect BibDesk to be able too find back linked files when they so rigorously move them).
As BibDesk first looks at relative paths, I would first try to arrange things so that the *relative* path between the .bib file and the PDFs is the same as the last time you saved the .bib file when the links were still working. Otherwise, you may want to move things back so the absolute paths are the same as that time. You may also want to use a backup of the .bib file when you do that.
If all of this does not work, you will have to link them back manually. The Orphaned Files feature may help a bit.
BTW, the AutoFile format is completely irrelevant, that has no bearing on finding the files, that’s only used when you auto-file the linked files.