@GoghGirl - I, too, used to have abbreviated series information in the title field for easy distinction when transferred to an e-reader. As you have discovered, though, this formula doesn't agree with a lot of the automated feature of calibre and its plugins (the one that tripped me up was Find Duplicates). Per kiwidudes recommendation, I looked into plugboards -- as PeterT and dwanthny have both suggested to you.
This is the thread where I got some much-needed help in designing a plugboard that would suit my particular needs.
As for the problem of manually deleting the abbreviated series portion of your title field, I would imagine that there was some reg-ex expression that could automate that for you via a search/replace. If there isn't, I've got another option: the one that used. Since most of my books had ISBN information, I did a metadata download (Amazon/Google/etc) through calibre with all the download options unchecked except for "Title". The metadata download would match the book based on the ISBN, find the correct title (ie the one that didn't have my personally designated series info) and update the title to reflect that. Naturally, I was only doing the metadata download on the books that had series information in the title, and usually in batches of 50-80 so I could catch any errors.