i saw this in the log file.
i removed all those --exclude for readibility
as expected, rclone complains about "Failed to create file system"
but then rclones seems to start to copy files.
2020/05/21 14:33:11 DEBUG : rclone: Version "v1.51.0" starting with parameters ["rclone" "sync" "/home/mathieu" "onedrive:backup_home/" "--links" "--delete-during" "--progress" "-vv" "--log-file=/home/mathieu/Downloads/rclone.log"]
2020/05/21 14:33:11 NOTICE: Config file "/root/.config/rclone/rclone.conf" not found - using defaults
2020/05/21 14:33:11 Failed to create file system for "onedrive:backup_home/": didn't find section in config file
2020/05/21 14:33:11 DEBUG : .config/chromium/Default/File System/002/t/Paths/000003.log: Size and modification time the same (differ by -967.919624ms, within tolerance 1s)
Dear @asdffdsa and @Animosity022, thanks a bunch for pointing me in the right direction! There was indeed two rclones running at once… When I started using rclone, I added to anacron, so it would run everyday when my computer is not too busy. And that's exactly what has been happening!
My apologies for the time you spent on it. I actually forgot I did this — It was my intent all along, but I did not remember I followed through and actually set it up. I have now removed the anacron entry, and resumed the sync. I can only assume this will be working well, and consider this issue closed (I will report if otherwise).
Now for anacron, this is a whole another problem, which I need to pursue now: How to run it as my user, so it can find the config file and copy as mathieu and not root. But that is for another day. Thanks again for your patience with my problem, and helping me find what was going on.