@Ian Waters Sorry for the painful experience. Just wanted to check few things to isolate the issue.
Ensure that the resource group where this migration project/recovery services vault exist is not being applied any resource lock (cannot-delete lock/read-only lock)
***I wonder if I need to just stop replication and start again?****
When you stop replication, the Azure Migrate: Server Migration tool cleans up the managed disks in the subscription that were created for replication. This happens only when the migration is completed. But in your case the test migration failed and I think it will perform clean up operation, post that you should be able to start replication again. I personally haven't tried this but since this is test migration you may give a shot.
Does it do anything to the onprem server like remove it or anything I would not be expecting?
It doesn't do anything unexpected.
Let me know how it goes!