Ok, I copied the German ebook into the English DB: no problems there (same columns etc.) and the German version has the current date in "modified".
Connected ereader to synchronize and, surprise

:
- calibre marks the German ebook as being "present" on the ereader (while it is not there yet)
- callibre marks the English ebook as not being present on the ereader (while it is actually already there)
The calibre IDs of both books differ, the German one being higher (newer) as expected.
So the matching process seems somehow to use a different approach than expected.