Hello fgossart!
I suggest you to have a look at our
Incremental Migration with ZxBackup guide to see how to perform consequential imports on a live system. Unfortunately restore operations do not perform deletes, so any item imported on the destination server and then deleted from the source server will not be deleted.
I'd like to better understand the situation, tho... You said that a lot of previously deleted items were restored: were those items deleted during the migration (in this case, see above) or before it?
Have a nice day,
Cine
the ZeXtras Team