Multiple arduino boards stopped working

Hi, we have 2 different arduino's board on our setup. We use them connected to Bpod to drive behavioural tests.
Yesterday I've connected a new Arduino board to the same pc with the only purpose of uploading a code on it. The new arduino board has been disconnected and from that moment on the previous 2 arduino boards stopped to work.

The previous boards are correctly recognised by the pc (right port number) is it still possible to upload codes on them without errors but they are not triggering the signal. We tried already to reset the boards and to change them to a completely new board.

We also disconnected one board at the time, proceded with the reset and test them out separately.

We thought something must be odd on the computer settings, as the computer is detecting the boards but not the signals out of them to trigger the last component of the circuit.

We are not arduino experts so we need help. Thank you in advance.

We are willing to try anything.

You are the only expert around for your project. We need to be educated! Begin with a block diagram showing all the devices, including power supplies and show their various connections.

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Which board(s) are you using? On what operating system? Which version of the IDE? Have you tried a different USB cable?

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Hi this is a module diagram

we are using 2 Arduino Uno, one of them has a Motor shield on top. The operation system is a Windows 10, the version of IDE is 2.0.1. yes we tried different USB cables as well as different boards

Could you rotate the image please so that it has the correct orientation?

But you need TWO separate programs running in the PC at the same time, to talk to the two different Arduino boards.

The second arduino has no code on it (empty sketch) it only serves to receive an input from bpod. I hope it's clear what I mean

Rotated image

Maybe I missunderstood you, but this seems not clear to me:

With an empty sketch load to it the ardiuno simply does nothing. Neither receiving anything nor transfering something anywhere else.

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I think that it means that the second Arduino only acts as a serial-to-usb converter. @regoloeleono can confirm that.

The usual way to do it is by keeping the second Arduino in reset (see the loopback test).

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