Loss of USB connection after flashing Zephyr image

Question

Hello! 
 I'd like to briefly introduce what I'm attempting to do: I'm trying to flash some samples from the Zephyr project into a custom board. The custom board is based on the RAK5010 which is supported by the project and uses nRF52840 as the chipset. 
 I am capable of building the samples from Zephyr and can see them work on the nRF52840-DK. So regarding setup for compiling and flashing, I believe I'm with the right setup. 
 The issue that I'm seeing is that when flashing a sample to the custom board, I'm "losing" connection with the USB. 
 For instance, this is what I have before flashing the "hello world" example: 
 
 ====================================================== $ ls /dev | grep ttyACM ttyACM0 ttyACM1 $ ls /dev | grep ttyUSB $ ======================================================

As you can see, there are 2 devices connected: ACM0 is the microusb connection with the board, while ACM1 is the connection done via JTAG. 
 I cannot flash to the custom board directly without a JTAG, as the tool isn't capable of seeing the board with the nrfjprog --ids command. However, using the JTAG I can flash and the flash is sucessfull as can be seen in the following logs:

====================================================== Flash output ====================================================== $ west flash --erase -- west flash: rebuilding ninja: no work to do. -- west flash: using runner nrfjprog -- runners.nrfjprog: mass erase requested Using board 59400959 -- runners.nrfjprog: Flashing file: /home/rys/Documents/repositorios/poc_nrf52840/zephyr/build/zephyr/zephyr.hex Parsing image file. Erasing user available code and UICR flash areas. Applying system reset. Checking that the area to write is not protected. Programming device. Enabling pin reset. Applying pin reset. -- runners.nrfjprog: Board with serial number 59400959 flashed successfully. 
 ======================================================

Now even though the board has been successfully flashed, I cannot check the logs or anything like that as the device is no longer listed: 
 
 ====================================================== $ ls /dev | grep ttyACM ttyACM1 
 ====================================================== 
 
 As can be seen above, only the connection with the JTAG is detected. 
 
 As for what I've tried so far: I checked the device tree file and the pin declaration is matching what I have on the board. I also tried to flash without the JTAG, but the board is never recognized by the nrfjprog tool during "west flash". 
 Finally, I tried flashing the blinky sample on the board to see if, at least, I could see the LED blink. If so, then I would know that at least the code is running on the board. However, even though I'm capable of compiling and flashing successfully to the board (at least according to the logs), I cannot see the LED blink. 
 
 Do you have any ideas on how I could proceed into debbuging this matter? 
 
 Thanks! 
 Renato