For vsa I schedule a job in the morning after all our nightly vms get backed up. I chose the advanced options to backup partial and failed vms. Its my safety net for the random missed backups at night. Not to sure on the file system side what we could do.
Use the Java GUI
Go to the subclient or backup set
Right click and backup
go to advanced
Select Backup failed VMs and include partial vm
click ok , then schedule this to your liking.