Hi Evros
I don't have much information, unfortunately. What I would suggest is trying to keep the memory reads (by the GUI/DLL) to return the same width and alignment of data even though the FIFOs are narrower. Just pad things out to the same width as the original design. Then the Wavevision DLL, script etc. should work though you'll need to be careful about choosing only the smaller capture sizes since the FIFO isn't as deep as before.
Let me know if that makes sense.
Best regards,
Jim B