@parasit - My comments were in relation to the previous suggestions on this thread, discussing the likes of robocopy, rsync etc. It sounded like you intended to sync the directories and then modify the database, which isn't going to work for the reasons I outlined.
As for what you have now described, I think you are still going to have a lot of issues. For instance your original post mentioned updates, not just additions. What do you do when books are renamed, by a title/author/series change? Or a new version that is under a different id? I think you are pushing the proverbial uphill but my only intent was to warn you that it is not a trivial exercise in case you wasted a lot of time finding that out for yourself
My personal recommendation would be that instead of trying to compare the databases with external tools etc, that you instead just put a shared directory that you use Save to Disk with, one for you, one for the wife. So when you add a book yourself to your library, you then use Save to Disk to put it in the shared directory that your wife can then do an import from, and vice versa. Setup your automerge options to replace an existing version. You will still get caught out if one of you renames an author/title name, but you can catch that with Find Duplicates plugin.
Stick the shared directories on something like Dropbox, and job done. It is how I share books with friends/family - they just perdiodically import into Calibre from the shared folder specific to them and remove the books from it when done.