There are companies who prep only, whether it be shot blast or diamond grinding. Might be worth the cost to get professional prep and do the coating yourself. Another option, if you have the head room, would be to lay down approx 4" of concrete and seal it after it's poured. We poured a new...
We used a lot of euchlid's joint filler in commercial buildings, but never used any of their epoxy coatings. You should be able to go to the website and look up the tech data sheets. That will give you a good idea of what you have, and also what applications it is meant for.
Is the base coat of epoxy with the flakes coming up? Or is it the sealer/top coat that is coming up?
I think after waiting 72 hours for the epoxy to cure you would've missed the re-coat window and would require some sort or sanding before top-coating.