Cyclone V: switching between application images using altremote_update

I'd select 'passive serial' probably with 4 bits. You'll probably find that the output file doesn't change (the .rbf ones don't).

Our build is set to generate the .pof and .sof by default - dunno where/when that got set.

It also isn't at all clear why the .pof and .rbf (and probably .jic) binary data differ slightly. The bits may not matter (provided the overal checksum is correct).

I'd try writing the data you've read back from the epcq for an image that loads.

And, if you can, do a readback of your written image.

You might have a timing error - so reads/writes are occaisionally corrupted.