De Tags von YEP haben nichts mit den SPotlightkommentaren zu tun. Man kann das eine in das andere Konvertieren, es ist aber unabhängig voneinander.
Handbuch S.31:
Yep keeps its meta data in an XML plist file in the follwoing locations:
The metadata for all the PDFs on the boot volume are stored on the boot volume in
~/Library/Application Support/Yep/docInfo.plist.gz
with a record of all your collections in
~/Library/Application Support/Yep/folders.plist
The metadata for all the PDFs on any other volume are stored on that volume in
/Volumes/otherVolume/Library/Application Support/Yep/docInfo.plist.gz
These are the most important files to backup.
The other data in the Library/Application Support/Yep folder are all cached information that Yep
can easily generate itself. (There may be PDFs in the Pending Documents folder, though).
Since Yep neither moves nor copies your PDFs anywhere, you just need to follow your usual bacprocedures for these documents.