It is highly recommended to run a clean either before or immediately after the installatioin of a new version of remastersys. This will ensure that nothing is leftover to cause issues.
It is also highly recommended to run a clean if you change the boot type - ie. ISOLINUX to GRUB or vice versa.
I won't make this automatic since some folks may have forgotten to copy their previous iso's beforehand and I don't want to wipe those out.