It's a good question. When I talked to the shop he said that Honda used to recommend just replacing the fuel pump and cleaning the tank, but now they also recommend replacing the injectors. The Repair Order does state Relace Fuel Pump per Honda. Replace Injectors Per Honda. Clean Tank per Honda.
So it would seem that replacing the injectors is actually an additional task from the infancy stages of the issue.
Perhaps they were finding that it was making it past the filter after all?
Edit: I don't think it was long starving for fuel. I had one incident of it acting up about 2 weeks prior to this last bout (where it acted up 4 times.) The first time it happened it was on the way up to Eisenhower Tunnel and I thought maybe it was maybe just some "one off" fluke with altitude. It seemed to run fine for two weeks after until the recent bout where I took it in. It never actually stalled or stopped running on its own, so it never ran dry. While it did happen a total of 5 times where it acted up, it was only encompassing 2 days.
The injectors were not done on mine last spring, which now makes me a little nervous. Could you do me a favor and scan/send a copy of the work order as that might help me if I run into problems myself? Thanks.