For its internal settings, Hazel keeps aliases to folders and such. If the folders are all replaced, it's possible that the aliases won't resolve at that point. Your rules should still be intact; check the Application Support folder for files with the .hazelrules extension.
To restore in this case, move those .hazelrules files somewhere else. Now, re-create your folder list. For each of the rules files, drag one in to see what rules they are (unfortunately, the filenames aren't easily mappable to the folder they belong to, at least for a human). Once you know which rules they are, drag those rules to the proper folder.
Post back here if you run into any problems with the above.