It's possible that the pore got blocked for various reasons, one of them could be that. You can try to increase pore size or use a low binding protein filter.
Prepare the dilution and keep it on ice. To avoid it to polymerize -blocking the filter- do the filtering immediately, keeping it at a temperature where it reminds liquid. If you have large volume do it in steps with a quick intermediate washings with a little volume of your diluyent buffer to clean the filter for the next round.