Welcome to the forum @PrettyPony
was a similar recent topic. I think the problem is in
It may think that a folder which starts with some other source is a subfolder.
It might just be a folder which starts with the name of a file, and not a folder.
This doesn’t seem to matter. Adding a filter may, as case is coded differently.
Any of the cases there will wind up saying something like this in Verbose log:
2026-08-19 09:41:18 -04 - [Verbose-Duplicati.Library.Main.Controller-RemovingSubfolderSource]: Removing source "C:\backup source\main\main.lrcat-data\" because it is a subfolder or subfile of "C:\backup source\main\main.lrcat"