I think it would depend on both epoxies. If the new product says it can be applied over existing coatings, you should be able to scuff sand the existing coating with a 60 grit sand paper to create a mechanical profile, remove the debris and apply another coating. Solvent based systems typically "bite into" or chemically attack the existing coating to form a chemical bond as well as mechanical. If the water based it unable to withstand this bond, it may wrinkle or blister from the solvents. Always safest to check with the manufacturer for recommendations.
