When Trying to clone the Fedora-32 TemplateVM, after two minutes, the operation is aborted with the message Error while cloning quebe, file pool cannot export dirty volumes. This happens independently from having AppVMs based on this template running or not.
It also seems that cloning is much slower in R4.1 than in R4.0, but this may be a personal impression.
For the legacy ‘file’ (not ‘file-reflink’) storage driver, it’s generally unsafe to clone or a back up a running VM. R4.1 has a new check to prevent this - which will also trigger if the VM wasn’t shutdown cleanly, so you may have to restart it and then shut it down again if that’s the reason.
You can install R4.1 on Btrfs or XFS and it will automatically create the /var/lib/qubes storage pool using the modern ‘file-reflink’ driver, which does not have these limitations.