SonnyK - if it's a public folder, the described process will take care of it. There are no exceptional PFs that somehow dodge the efforts of the script.
Note that there are some PFs which do not have a replica list (and hence no content themselves). Given this, the script makes no changes and there's nothing you need to worry about.
The bottom line is you need to look in Public Folder Instances (or on Ex2007 servers, get-publicfolderstatistics) and that list will slowly empty out. Once empty, the process is done. No other manual effort on your part should be required, outside the possibility that you've got a persistent replication problem which needs diagnosing (see Bill Long's extensive blog entries on diagnosing such problems).