Well, I'm happy for you..🙂 I've never had much if any luck with that type of stuff.
Depending on the age of your waders and the original quality of your booties, leaks in the neoprene (that cannot be tied to a visible tear or puncture) are usually compression leaks that are a natural result of material fatigue over time. If this is the sort of leaks you have, you'll probably be addressing new ones from time to time as your waders continue to age. You could certainly continue to use Flex Seal on them with acceptable results. The only caution I'd have about this is to make your applications light enough to avoid enlarging the bootie to where the fit inside the wading shoe starts to become a problem. This happened to somebody I know who lives at the same address I do.. But certainly not me. I have more common sense than that.. Or at least I'd think I would...🙂