I doubt it removed any Rain-X but I would use Rain-X washer fluid instead of reapplying.
I could never get Rain-X to apply without smudging. I had to clean it with their cleaner a few times to remove those smudges. After that, I started using Rain-X windshield washer fluid. Initially, I used to add concentrate to the washer fluid, not anymore. As long as I keep the wipers clean, I don't have to 'apply' Rain-X.