I have mentioned many times that an epoxy primer CAN have a reaction with an acid like Ospho, which is a phosphoric acid solution. A second coat neutralized by water is the answer there. I was first told this by the man at Southern Polyurethanes. I have tried to say on here also, there is also a difference in auto cleaning acids types and "rust convertor".
Just wondering , did you use an acid product to clean the metal or a rust convertor. But like you said, he problem will arise IF there is an acid in the epoxy that reacts to the acid cleaner. Just wondering.