HI Marlon :
i think swapping bytes come from using SGDMA (when it read and write data on memory), So you should swap bytes in
input and output of FFT.
i think it is not good way to swap bytes in software (by using pointers). maybe it spends a time from Nios II.
it is better to try swapping bytes in hardware, by swapping the signal in (fft_avalon_wraper.v) file. change the connect of signal to match your swapping.
for example, try to do that in (fft_avalon_wraper.v) file:
wire [15 : 0] temp_input;
assign temp_input[15: 8] = sink_real[7 : 0];
assign temp_input[7 : 0] = sink_real[15 : 8];
temp_input is the input of FFT module.
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you should do the same for output.