I restarted the server and sat and watched the copy job progress and resource monitor for about 45mins today.
As the backup copy job ran, the server got noticeably slower from a UI perspective and then stopped. Vsphere posted a virtual machine CPU usage error. While I watched resource monitor on the guest there was no sign of high CPU or memory usage.
I disabled the backup-copy jobs and restarted the server. The small backup job running in the site completes ok. The backup-copy job from that site to another site also completes ok.
I've got some new storage being install at that site next week, so will try moving the repository back to NTFS. There's about 50TB so the move will take so time