thanks a million davidfor!
So if I get you I should:
- sync both devices with the cloud
- connect both devices to my laptop, and transfer sideloaded books from the Mini to the Aura;
- save "UserKey" from Aura's KoboReader.sqlite ([I]to do so I've gone into "edit" and copied the value in a text file)
- run the SQL statement you gave me on the Mini KoboReader.sqlite file and save it in a file (CSV I think - this I tried on a mock file and I think I can do that)
- copy the Mini's KoboReader.sqlite onto the Aura.
- restore the csv file created in 4.
- restore (again, with edit, I copied back the cell value) the "UserKey" data saved in 3.
- disconnect the two readers with fingers crossed

Does this sound ok? Thank you!
EDIT Oops! Something went wrong... 
I did it all, but the import of the "dumped" bookmarks did not work (got an error message). Nevertheless, with my fingers tightly crossed, I disconnected the Aura, and trying to open a book I had finished, I got an error message (the book could not be found). Powered off and on, same error message. So did a sync, the Aura downloaded a ton of books. It does see the pdf files, but it won't open the sideloaded kepubs, although they are listed (I guess because of the database). So I'd say it did not work! Never mind, that'll teach me to dump the Mini...