Ok, some clarifications are necessary.
The USB serial interface from openpnp is located on the main board, installed on the machine bench. This board have around 60 analog and digital ports, one CAN interface, one RS485 interface. Ports are connected mainly to relays for feeders, RS485 and some ports are routed to servo controllers and CAN is going to head. On the head, there is another board which control 4 nozzles with steppers for rotation and Z actuation, position sensors and relays for vacuum ejectors. Both boards are based on a Silabs 8051 CPU. There is no signal integrity problem on the machine. USB serial connection is stable, cameras never disconnects. CAN bus is properly terminated, works without errors. Servos as well, there are chokes everywhere, as required by servo controllers installation guide.
The problem is that the board's firmware is work in progress. Everything is written from 0. My problem is not to debug something which is supposed to work. My problem is to write the firmware for the entire machine and I have some glitches in algorythms somewhere, and I cannot find them. Typically, a command received on USB is broken in pieces. Some pieces are for servo controllers, those are sent by main board to the servos. Other pieces are for head board, to actuate nozzles, sent on CAN, and there, head board splits them further into signals for stepper drivers. After those are sent, both main board and head board must be monitored for command completion, in position signals, end of stepper movement, etc. Sometimes (1 from 1000 placed components typically), this chain fails somewhere and I need to see where, by monitoring all the path from USB serial port to the other end. When I connect logic analyzer to the machine, it needs to be connected to both boards (base and head) to see the sequence of the signals. But I also need to put analyzer's ground on boards and to laptop and thus I create ground loops which destroys the analyzed signal. This is why I need to transport test signals from both boards to analyzer without electrical connection.
You can see the boards in the picture. They are actually identical hardware but the firmware is differentiating between main board and head board.