Duplicati errors: Tries to back up deleted folder - how to avoid?

Welcome to the forum @Kavito

The day before what? More importantly, how far before Duplicati backup start?

Is this a local filesystem, or something networked where file listings can linger?

Duplicati walks the filesystem. If it doesn’t see folder, it won’t attempt a backup.
A filesystem walk is not instant though, so make sure all settles before backup.

Duplicati will notice the folder’s disappearance, and consider it to be a deletion.

Is it ever on a far earlier deletion, or only on the latest delete (how far before)?
FileEnumerationProcess is the first step in a pipeline. It must have seen folder.
I’m not sure it should have passed folder on to the later pipeline stages though.

Channel Pipeline is a technical discussion if you care to get into it more deeply.