When you start the new sync it looks to see what is there first.
In general cloud storage systems don't support half uploaded files - they are either there or not there. So if it was only half uploaded, it won't be there at all.
You can't pause the upload for too long without the upstream provider timing out and killing your upload.
What you can do is make rclone run slower.
You can use the
--bwlimit schedule to turn the bandwidth down at times, and you can use SIGUSR2 to turn the bandwidth limiting on and off.