Yet Another CF/Verity Question....

I have a collection which indexes all htm, cfm and pdf (adobe acrobat) files under the root.  I would like the collection to be *completely* reindexed every night, as the website goes through many changes during the day.  I have it set up to run an indexing file at night, which simply has a <cfindex action="update"> tag.  That seemed to work for a while, until I noticed that it was only indexing files which have been added, and not removing files from the index which have been removed, or reindexing files which have been changed.  Soooo, I try running <cfindex action="refresh">, and now the collection is empty; I reindex using <cfindex action="update"> and it only indexes htm and cfm files, not pdf, despite the fact that I have the extensions attribute set to extensions=".htm, .html, .cfm, .cfml, .pdf".  So I try purging and reindexing using action="purge" and then action="update", and same thing.  The only solution I've discovered is to completely delete the collection and then recreate it and THEN run <cfindex action="update">.  However when I try to automate that with the aforementioned indexing page, it seems to delete the collection (doesn't show up on cfadmin page) but the directory is locked up on the server, which means I have to go in and stop/start the service before I can delete the directory.  Then I can recreate the collection and index it and it works fine.  But sooooo cloogy, not to mention a pain in the you know what.  Any ideas?