Ok I’m not a OneDrive user but I believe it has a limit of ~5000 files. One solution may be to increase the “remote volume size” in Duplicati from the default of 50MiB to something larger. This results in fewer files on the back end, but it has its downsides too. So you don’t want to pick too large of a value, either. See Choosing Sizes in Duplicati - Duplicati 2 User's Manual for more information.
Also, if you do increase the volume size, then with OneDrive I believe you may also need to increase the --http-operation-timeout value from the default (100 seconds, if I recall) to something longer. It needs to be long enough to allow for a larger remote volume size to be downloaded or uploaded within that timeframe.
Finally, note that changing the remote volume size only affects future volumes that are uploaded. So you may need to erase your backup data on the back end and start over to fix this.