According to kb2042, there is a bug in VDDK6 and its treatment of VMDKs with duplicate disk names
The workaround from Veeam, was to failback to NBD instead of hot-add
I contacted VMware to see if this was fixed in a newer version, otherwise I need to rename all disks, or move them to different SCSI IDs; changes that requires downtime
They said
We have checked internally, there are no such issues from VMware end.
I will ask support guys to update the article, if required. Anyway, as the KB says, if you're running at least Veeam B&R Update 2, there's nothing to worry about, since the issue was worked around there.
According to our information (VMware SDK support case 15684272306), the issue is still there and is planned to be fixed in VDDK 6.0 U2. I admit engineer you've talked to could confuse the issue with some other one.