Just verifying, the list DOES self-maintain if you edit all rule sets that refer to the old folder names. It's a bit of a pain, but Hazel does color code the folders in the list. Missing or "old" folders are lighter blue in color.
I have two "Hazel action" folders which use the same rule set, one on my home machine, one on Dropbox. I tweaked the scripts for the home machine, exported the modified rules, deleted all the rules for the Dropbox location, and then imported the modified rules. When this was done, my folder list cleaned up, and the renamed/deleted/missing folders disappeared from the folder list.
Hope that helps others.