Is 5259 roughly all the files in that folder? Please check the job log or emails for history of “KnownFileCount”. There’s a much-discussed 5000 file limit OneDrive for Business got from SharePoint that might be doing this.
Manage large lists and libraries in SharePoint
You possibly can also see in your job log how well the initial listing is going, by looking for something like this:
Messages: [
2018-09-07 12:28:04 -04 - [Information-Duplicati.Library.Main.Controller-StartingOperation]: The operation Backup has started,
2018-09-07 12:28:05 -04 - [Information-Duplicati.Library.Main.BasicResults-BackendEvent]: Backend event: List - Started: (),
2018-09-07 12:28:05 -04 - [Information-Duplicati.Library.Main.BasicResults-BackendEvent]: Backend event: List - Completed: (36 bytes),
to see if your listing got very long, really short, or failed. You might need to set --log-level=Information for this.
The initial listing check can be suppressed, but I’m not sure how advisable it is to just try to live without listing.
–dry-run might make tests safe enough (to see if things get further), but lack of lists might break other things.
List large folder in Onedrive for business (od4b) #2580 is a similar problem where an empty list was returned.