To rectify this I will be creating new .vhdx files on a different storage array, creating new Exchange databases on these .vhdx's and moving mailboxes to the new database.
In B&R (v9.5 u4 btw) Veeam just sees the VM you are backing up and not the .vhdx files associated with it.
This particular backup job is a normal backup, replicated to another Hyper-V server, and a backup copy sent to a cloud repository.
I pretty sure I know the answer to this, but will ask anyway

Since I am moving and enlarging all the .vhdx files associated with the VM, I will need to create new Active Full backups, stop replication and delete all replicated VM's on the repository server before starting a new replication cycle, and create a new backup copy job for the cloud repository.
Otherwise my backups/replication/backup copy will fail due to the differential in .vhdx size correct?
Thanks for any input!
- Doug