This is the message I sent to support.
"In both the veeam backup and replication job, we had an excluded disk in the job. Basically, we were excluding a drive that contained tempdb, which is useless to replicate or backup in my opinion as it is simply just recreated anytime mssql is restarted.
What we ended up doing a few months back is deleting the disk from vmware and then recreating it. It was too large for our needs so we made it smaller.
I believe this to be the cause of the issue. Veeam didn't really complain because the disk was excluded. My guess is veeam only concerns itself with the disk number (ie scsi 0:0 etc..). It doesn't really check if it is the same disk or not. So when I deleted the disk and then re-added it in vmware, the number remained in my case scsi 0:2. Veeam saw that it was only to worry about scsi 0:0 and scsi 0:1. But, somehow scsi 0:2 is relevant to veeam even though it is skipping it.
To test this theory on the backup job, I removed the exclusion. The backup did not give me the message "Virtual disk configuration change detected, resetting CBT" for one job, but it did for another. In all cases, the job worked correctly at least after the second run. After the second run completed, I again excluded the disk and now it is running normally again.
I wanted to test one other thing, could I simply just remove the exclusion and then save the config, then just re-add the exclusion and save the config again before starting the job to see if I would get the same result? That did not work for me, the job had to run once with all disks before I could successfully re enable disk exclusion.
Replications seems to be a different story.
When I removed the exclusion from the replication job, on one job it failed with "Processing configuration Error: Cannot replicate disk [XXXXXXX-LUN6-DG4-TEMPDB] xxxxxxxxxxx/xxxxxxxxxxx.vmdk because its capacity was reduced" ie the disk size change as explained above. I tried it again after manually removing snapshots but same thing. I had to go into the replica and delete the disk (who's size didn't match the vm, it was still the old size on the replica). After running the job, it seems ok, it is running now but will take a while to complete and know for sure. I did not receive the cbt message but it did have to calculate digests.
On another replication job, it did recognize the disk size change and gave a warning "VM disk size changed since last sync, deleting all restore points". It proceeded to delete all replica restore points. Then, it added the new disk to the replica, but did not remove the old disk. I have to manually delete the old replica disk once the job finishes."