you need to change the shortcut they are using and let it use your new shiny process. It will still use the old one until you have done this.
Also if you deactivate the old one, any existing processes might give the odd error. I'd look at putting in a reinitialise action in the old process to allow you to switch it to your new one
DMS, I forgot to include, I actually used the same name as the original one. I renamed the original to another name and use its name to the new process. Just out of curiosity, would it be fine if I were to just edit the original one instead?
My advice still holds, even if you are changing the name back to itself, LDSD tends to use a guid to remember things and so by editing the shortcut and changing the process to be itself again, that should work, or create a new shortcut.