I have the same thing, You can stop it by sealing the floor. The only issue is the expoy floor may not stick.
I'm not sure if the epoxy will do the same thing, Maybe you can test a small spot to see.
Good luck on your build!!!
Why not Pour some self-level down on the old floor to get that smooth finish? A Concrete based self-level should do the trick for you. Just make sure you prime the floor before pouring.