Enable/disable/pause gl.inet firmware using /dev/ttyUSB2

we are using X300B in our industrial products.
We need to implement a phone-alarm system using SMS and call(without voice).
Everything is working as expected using /dev/ttyUSB2 in our C application running on the device.
The only problem is that /dev/ttyUSB2 is also in use from the gl.inet firmware for reading the signal etc. for the webinterface.
When sending out a SMS, it can happen that the gl.inet AT command is included into the SMS as it was sending at the same time.

is it possible to disable the AT commands from the firmware for the time where our application needs the serial port and enable it after the process is done?

I guess the caller to access /dev/ttyUSB2 is from the Admin panel API. So you can disble HTTP server for a test. When you not access the Admin panel or Goodcloud, the conflict should not happen.