It's surprising how much junk you can get out of a filter before it starts restricting the fuel flow. Yes, I've been known to clean one out by shaking it and then putting back on when I did not have a spare one handy.
Assuming your guy put fuel in the filters, there is no way that small amount of fuel is going to clog the filter regardless of how dirty.
Thanks for the update although it's still a mystery why the filters caused the problem. Two expensive filters is still cheaper than a visit to a shop. I would put one back on at a time to see which one was the problem and then cut it open to see if there is a obvious problem, but I like mysteries and the smell of diesel on my hands.