What 2 bypass valves?
Are you talking about the valves on water heater?
Are they attached to the PEX line using bands?
If banded......cut band into diagonally across band carefully. I know PITA to access. But if you cut almost all the way thru then you can twist them off.
Then go buy some Sharkbite shut-off valves......3 of them
Install one on cold inlet, one on hot outlet and one on line that connects cold/hot (bypass line)
Sharkbites just snap on, Don't leak and are very good quality. Home Depot.
Lowes carries similar called Gatorbite
The End of PEX needs to be clean straight cu and no burrs.