Verify that the diagnostic monitor works (as described in the same page) and note down the versions for FPGA logic and NIOS int the "WAVEGEN status" tab.
Stop the log monitor.
Step 1:
From the drop-down menu select "Flash clear"
Enter the following parameters: "user logic", start dsp 0xFA, end dsp 0xFA. Check "want reply".
Click Send. It will take a few seconds before a reply appears in the log window at the bottom. It must have code "c8" ("c9" and "ca" will signal an error).
Step 2:
From the drop-down menu select "Flash write same"
Enter the following parameters: "user logic", start dsp 0xFA, end dsp 0xFA. Check "want reply" and "create multiple packets".
Select the correct RBF file. For SOUL, it's WaveGenLogic_6_04.rbf
Click Send. Verify that all replies in the log window at the bottom have code "c8"
Reset the BCU47 (or power cycle it), start again the diagnostic monitor, and verify that the FPGA logic version has changed.