Can you explain what you mean by collection? Are you referring to all the ebooks on your Aura as a collection or are you referring to adding books to tagged groups by whatever criteria you select (genre, author, series, whatever).
At a wild-eyed guess, it would appear that you had a crash after which your Kobo did a factory reset which would remove all sideloaded books and you are saying that ebooks that you are sending after the crash are not being seen.
If you are using calibre with the KoboUtilities plugin installed, you can use it to check the database.
A couple of quick items would be to power cycle your Kobo to force the database to be reloaded and, if using calibre, to check that in Preferences under Sending to Devices, metadata management is set to automatic management.
Last edited by DNSB; 08-09-2023 at 12:17 AM.
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