There was hope (and some test evidence) in ‘No files were found at the remote location’ using Onedrive for business that the 5000 limit was removed when Duplicati switched od4b to the Graph API in 2.0.3.4 in April. Are you still seeing issues arise at 5000 files when using a recent enough OneDrive For Business release?
I have no immediate idea on the rclone aspect (I don’t have a configuration like that), but do you know if the rebuild problem depends on large destination size or file count, or can it be reproduced on a small backup?
Possibly another way to test would be Restore → Direct restore from backup files, which makes a small DB.
If there’s a problem with rclone as a backend, there should be some evidence, maybe in About → Show log → Live → Information (which should be enough to show transfers of backend files, or the lack thereof…) or –log-file with –log-file-log-level=Information (or even higher, such as Profiling, if lots of output is tolerable…).