I checked the BI situation on the HAM-A coil driver. It seems like these are sinking BIs and indeed need to be isolated from the Acromag unit GND to avoid contamination.

The BIs will have to be isolated on a different isolator. Now, the wires coming from the field (red) are connected to the second isolator's input and the outputs are connected to the Acromag BI module and the Acromag's RTN.

I updated the wiring diagram (attached) and the wiring spreadsheet.

In the diagram, you can notice that the BI isolator (the right one) is powered by the Acromag's +15V and switched when the coil driver's GND is supplied. I am not sure if it makes sense or not. In this configuration, there is a path between the coil driver's GND and the Acromag's GND but its resistance is at least 10KOhm. The extra careful option is to power the isolator by the coil driver's +V but there is no +V on any of the connectors going out of the coil driver.

I installed an additional isolator on the DIN rail and wired the remaining BOs (C1:SUS-ETMY_SD_ENABLE, C1:SUS-ETMY_LR_ENABLE) through it to the DB9F-4 feedthrough. I also added DB9F-3 for incoming wires from the RTS and made the required connection from it to DB9F-4.

I tested the new isolated BOs using the Windows machine (after stopping Modbus). As before, I measure the resistance between pin 5 (coil driver GND) and the channel under test. When I turn on the BO I see the resistance drops from inf to 166ohm and back to inf when I turn it off. Both channels passed the test.