Anything you set in LimeSuiteGUI will be lost when this closes the connection to the SDR and something else opens it and resets the chip.
There is a previous discussion on AGC setting here:
@zack or @garmus may be able to comment further.
When using GNU Radio we would generally advise use of gr-limesdr source/sink blocks, which do not involve SoapySDR, which is an abstraction that sits on top of the native “LMS API”.