We have been severely affected by this CBT issue I believe as well.
After updating everything to ESXi 6.0 and Veeam 8 update 2, we ran our first backup against all of our Vmware virtual servers.
The first thing we noticed was that our backups are now super slow...that wasn't the main issue however.
After a full Exchange backup finished and the snapshot merge took place, 2 of the 5 mailbox stores dismounted.
It took Microsoft to get the stores back to usable and mount. After dealing with that we ran another backup(not knowing what the root cause was) on Thursday night.
This took 4 of the mailbox stores offline, and even microsoft couldn't bring them back, too corrupted...We restored that backup and recovered the databases with eseutil /R, and all databases now mounted and mail was flowing again.
We are now in the process of migrating all user mailboxes to a new virtual machine and new mailbox databases for fear the corruption is deeper seeded. We will use Windows server backup to backup exchange until Vmware fixes this critical bug.
I have cases open with Veeam and Microsoft, but I now believe the issue lies with CBT and snapshot merge with Vmware.
We updated because of a Server 2012 reboot issue which was fixed in 6.0, but the cost was far too high.