The qubesd daemon have no information about clone source - from that
side it looks like a new VM. This means application menu is created as
for a new VM.
To fix this re-initialize menu with --source option as part of the clone
operation. It will copy both list of available applications (if
applicable) and selected applications.
This fixes both qvm-clone case and rename.
FixesQubesOS/qubes-issues#3902FixesQubesOS/qubes-issues#4124