There are 2 types of water heater bypass systems, the 3 valve - 1 each for in, out and bypass between the in and out. A fool proof design.
The other is a 1 valve bypass to inlet that then switches flow to bypass and depends on a auto check valve at outlet to close to prevent inflow to the cold water heater tank.
Failures are rare of manually operated valves, check valves do need a good slam of pressure to close. Build up your air or pump pressure to maximum before bleeding the water.
When pumping the pink be certain all valves are in winterizing position ( CLOSED) Run the pump until it pressurizes the system to cut off, then go- slowly- to each tap nearest to farthest , 2 times around allowing the pump or compressor to rebuild pressure to each tap
Edit, I think you pumped a/f too soon, without enough pressure to close the spring operated check valve.