I have to deal with this in magazine work all the time. InDesign is better at it than Quark was, because of the ability to lock and release master page items.
Two suggestions:
1. Until you're sure that you actually do need to switch your pages from left to right, use the Numbering & Section options to create sections that start verso or recto – for instance you can do this on page 20 and lock it to a left page, then move the 1st 20 pages around without impacting anything after page 20.
2. Once you have all the pages flowed, you can delete the “active” text boxes from your masters. Leave the footers, and any elements that haven't been modified or “released” on the actual pages. Then, if the pages move left and right, the master pages won't reapply a copy of the live items and the locked items will move to the correct position based on the master, because they are still locked.