Hello @martywittrock
As far as I can remember the FPGA programming is done by LimeSuite GUI . Alternatively, there’s a command line tool that does the same operation.
I had to program the FPGA using a JTAG programmer only on my LimeMini, and only one time, just because it was a pre-production one. If you were already able to update the board using the GUI then I don’t think you need this.
Instructions start more or less from here if you actually need to do that: Problems with LimeSDR mini
mario