Hi Christopher,
Sorry to hear about your issue.
Perhaps this post can help you find a (possible) rclone (write) cache containing files that haven't been uploaded yet:
https://forum.rclone.org/t/cant-find-cache-folder-on-windows/15186/7
If not, then please share the exact mount command used, that is something like:
rclone mount myS3: ...
How many percent of the files do you see in S3 when using a command something like this:
rclone lsl myS3: