Neil, can you tell me which version you're using? I believe that as of version 1.10 the add-on pretty much replaces old signatures wherever they are in the script. This means that in a long thread, it should just find the old signature in the quoted text and replace it with your current signature. Version 1.11 supports up to 4 signatures per address, and you can specify what those 4 signatures should be labeled, so you could set up a "blank" signature for each address that you could select any time you want to remove the signature. It's not very easy to explain, but you'll see what I mean when v1.11 comes out.