OK, so after reinstalling the XWiki standard flavor didn’t help and I didn’t bother to go through all 289 changes one by one, I again installed a fresh wiki with a new database and imported only those pages and admin sites where I was certain I made changes (I secured the few pages that were created in the meantime by hand, since the Export/Import section was missing through the admin menu).
It was a bit of a pain in the ass, as these sites are indistiguishable to the default ones except by the naming. But now everything seems OK, nothing missing and no errors.
So I can only assume that my old export included somehow many pages more than I’d selected. I remember chosing that option " Created and modified pages" and that I had to scroll down to select more of my own pages (since they weren’t all ticked). When I go back now to export now there are way less pages listed (only my own ones).
I’m glad that I managed to get everything working now without errors or missing settings and I’ll be wary what’s selected during export the next time.
Thank’s for your help!