[mathil]

@ZodWallop have you tried 'resetting' your collections? Disable Collections from Kobo Extended plugin, upload metadata, then Delete empty shelves via the Kobo Utilities plugin (and if that doesn't work, do that manually). Sync to your Kobo account and see if they've been deleted there too (if they haven't or if there are some left over, delete them manually - I've done that before through the Android app). Then, re-enable collections on the Kobo Extended plugin and upload metadata. If anything it should still take less than resending all your books over.