Hello,
this is intended because the same UUIDs are used for the sync. Backup restoration is supposed to reset the online status, but using the same UUID may lead to issues because of how CloudKit and our sync are conceived. The UUID in the backup’s single files is used to change the internal note-linking when a backup is restored. Unfortunately, this applies only to the note links in Bear and not to external apps.
Theoretically, we can overcome this limitation but means heavily changing the sync and potentially generating more issues. Also, this doesn’t seem to be an issue for many.