thanks for helping.
I use ISBN because when creating epub with write2epub I can write in ISBN metadata the version and it is automatically recognize by calibre if I display the column ISBN. And also because I have my own book and don't use at all the ISBN feature. that's why I was focused on ISBN metadata with pdf.
But I could use another one (simple custom column called myversion) if I know how to fill this column automatically by calibre when importing an epub or a PDF (from version stored in a pdf or epub metadata)
- I wont create a new version of calibre.

- Why not using command line program and some scripting. for example : I add a lot of pdf and I run a tcl script that refresh calibre metadata from imported pdf.
let's ignore epub version becase it works simply using ISBN.
For Pdf you sent me some TCL commands but I don't know if I could use them because :
ebook-meta : read only a selection of metadata so no "custom" metadata
set-metadata : write a metadata in the opf file (calibre metadata) but this feature is already included in the ebook-meta command.
you were speaking about XMP metadata in pdf, can Calibre read them ? even if it is custom metadata ?