Probably the hall interface board ( in a black box separate to the controller) . As it sounds like you know, the boards for car buttons and hall buttons are not interchangeable although they look nearly identical . Put the wrong one in the car and you will damage the motherboard behind the COP .

Hall board LD latch light is lit on Hall interface board is the touch tone board on the HIB or the main COP board?

Tone generator board is in the COP

In your hall interface board bottom right hand side is a resistor it will read good on meter but actually is bad will cause same issue cheap to replace an good idea have extra on site

I have 3 hall boards in MR it's a duplex with single riser should I replace resistor on all of them?

check the prints, some of those hall board are for hall lanterns. if it s a duplex, then you will have 2 boards for hall lanterns, one for each car, , and 1 board for the hall calls that the 2 cars share. just determine which one is for hall lanterns, and swap that one with the hall call board. there exactly the same. that way you will have hall calls, and don't worry about lanterns if you get lucky, the bad channel will not be use not the lanterns circuit, and you can continue on if not just have them repaired. fairly simple circuit should not cost to much to fix thats what i would do. that way you will know if the HBI board is bad, or if you have damaged the tone generator board, or the car cpu. good luck

Replaced with correct board and both cars had to be resync and turned back on in correct order. Hall lights now latch but still problem with car PI not on and hall PI is on but,segment display showing corrupted binary.