Presenter '09 and IE11

I'm hoping someone who is still plugging away with good old Articulate '09 like myself could help with this question.

We've been told we may be going to IE 11 in the next few months. Our IT department installed the necessary Articulate update and also gave me the Articulate IE11 Updater Tool. I ran the updater on all our published zip files and updated them, so that's all done for our current published courses.

When I open up a previously published course PPT to make a change and republish, I still have to apply the updater tool, meaning that it is finding an update it needs to make.  However, if I create a brand new course, the updater tool shows that it is okay.

So my question is - Moving forward, will we need to apply the updater tool to any courses that we re-open, modify and republish? 

I hope this question makes a little bit of sense. I have major mush mind right now. We're getting ready to implent a new LMS and I've been doing nothing but learning new LMS lingo and testing for the last month. 

thanks!