MobileRead guidelines forbid us from discussing DeDRM tools in-depth... although we can discuss it in the abstract, so it might be worth noting that as a filetype plugin it only runs when you import the book, NOT when you convert the book. Any actions such a plugin might take would of course apply if you delete the book and re-add it.
Further discussion should take place on
Alf's blog. There is a comments section there, where help can be found.