Definitely follow their instructions to the letter. But here's what I'd consider...
Don't have a lot experience with your particular product, but a good epoxy should stay down, for a long, long time. It's not designed to fail at some set moment of time. I'm pretty certain you didn't go into the garage one day and notice that overnight chunks of your floor coating came up, and from that point forward the rest stayed down. No, the weakest parts came up first, then the slightly less weaker etc. over a period of time. So the question is: how can you be certain that the stuff that's remaining won't fail after you coat over it?
The answer is you probably can't tell. It's possible that the spots that have failed will be the only parts to lift, but there really is no way to tell. All we can say with certainty is that something went wrong, and the odds are more likely than not more of your coating will continue to fail.
You already put in time and money, only to have to put in more time and money in to it, make sure this time it's the last time. As great as the next application may be, even if you use better technique and products, it's clear the first coat failed, and there's a good chance it will continue to fail, taking the next coat with it.
You should completely remove that first coat. Grind, shot blast, or chemical strip, take it off because it doesn't make sense to let it compromise whatever you decide to recoat with.
And I'd look for a product that has a better track record of adhering to concrete.