Figured out a workaround and potentially what the trouble was. I totally spaced that I have the Feedburner Feedsmith plugin on to redirect all my feed subscribers to my Feedburner feed. Which means all these adjustments are unnecessary.
All I have to do is go to feedburner, click on the feed you want to change, click edit feed details, and then change the feed location through feedburner from this:
with the cat being the category number I want to exclude.
Works like a charm and makes the change without losing any subscribers or having to update any links, etc.
Hope that helps someone else.