Don’t throw away the RTV silicone! As mentioned, it lasts longer than flowable and I’ve used it many times over the years with no problem. Unless the yo-yo is responsive, those bumps don’t really matter in terms of play.
If you’re going to re-do your silicone, a tip I can give is to use a small spoon to create the recess in the silicone. Search on Youtube for Brandon Vu’s “How to re silicone a yoyo” video. It’s the exact same way I’ve done it over the years.