One easy think we could do is make the max number of items in a directory configurable. Then you could sync once with one value and again with a different value. Set them both to be prime numbers < 1000!
This parameter is available in some other backends already
--azureblob-list-chunk int Size of blob list. (default 5000)
--drive-list-chunk int Size of listing chunk 100-1000. 0 to disable. (default 1000)
--s3-list-chunk int Size of listing chunk (response list for each ListObject S3 request). (default 1000)
Do you want to have a go at this?