Yay, thank you.
It isn't as easy as I was expecting. It is related to "library discovery", which is just a glorified recusive dir iterator looking for calibre metadata files.
We have had the assumption that the root dir of the library contains the metadata, which holds true for stock drivers, connect to folder and wireless. It isn't the case with drivers and custom paths. Metadata might be several directories above documents, so we cannot longer trust on the calibre metadata file path to turn calibre lpaths into absolute paths.
It is, of course, fixable. Patches very welcome