I would like to make a fresh sys-whonix but I wonder if I delete sys-whonix and then make a new sys-whonix am I messing things up? Is there anything special about the sys-whonix that the system creates for me? I don’t know much about salt but is it somehow “tied” to the default sys-whonix?
Not from anything Whonix does.
Any potential bugs in Qubes dom0, I don’t know. That is best asked at Qubes support. As per:
In an ideal world, there shouldn’t be any issues. In theory, there might be issues. I didn’t run into such issues when deleting sys-whonix yet but in an earlier version of Qubes my dom0 got broken by removing an older, no longer used Fedora template (unreported).