[Otto]

I think I see what you're saying in your guess...

If you are doing a second measurement, and then allowing REW to find and apply filters, there can be trouble if you are already have filters engaged in the BFD. REW won't know what filters are on the BFD, so its newly determined filters (from your second sweep) will be off.

You can continue to sweep and tweak filters. I usually do it by hand, though. I tweak the filter values that were determined in the first sweep, reload them to the BFD, tweak again, etc.