Can the epoxy go over water based polyurethane?

We do not recommend putting the epoxy over water-based polyurethane. The epoxy could cause the water-based polyurethane to wrinkle or soften. Also, Epoxy does not stick very well to water based polyurethanes and you could end up with fisheyes (epoxy pushing away from the surface).  We recommend applying 2-3 coats of oil based polyurethane over the water based coating so that the epoxy will stick to it. It is also best to test it out first on a small scale test to be safe.