When transferring my backup to some offsite hard drives the drives run out of space before the copy can complete. There's plenty of space for the final product of the copy but it seems to do the deletions last when syncing files up.
Is there a way to get the deletions to go first in the sync process so it has that free space to work with for the new data?
Deletions of remote files are actually done before uploads.
Though synchronization is done by directories. So if the first synchronized directory has new files, while the others have obsolete files, upload from the first directory comes first. You may try to execute synchronization for different directories one by one.