Flashing check engine light on 02 Honda Oddyssey after Valvoline oil change?

Got an oil change at Valvoline, and next day check engine light began flashing. Car was running flawlessly before oil change.

They suggested a new fuel filter, as mine was pretty rough. I declined. Got error codes of random misfire, as well as cylinder 1,2,4,6 misfire. Scanner at auto zone listed EGR valve as suggested part.

Could this possibly be that the fuel filter is bad or was put back on incorrectly?

You stated you declined the fuel filter so why are you asking if it could be the fuel filter was put on wrong. Either way a fuel filter is not the problem.
With a flashing CEL the spark plugs are the first thing to replace. NGK or Denso Iridium spark plugs only! Are you aware of the common problem with Honda motors? Thy get tight valves and the valves need adjusting every 60,000 miles.Find a real mechanic and get the spark plugs changed and the valves adjusted. That's how I would approach the situation.

Check if any vacuum lines got disconnected. Check intake vacuum with a vacuum gauge. Vacuum is good, check fuel pressure with a gauge.

Examine what the OBD2 codes indicate. This is not related to oil change, unless you knocked something loose. Can't tell anything more without the actual OBD2 codes. Read up

Someone disturbed something doing the oil change.

I would not let any of those Oil Change Places touch my vehicle. Most are known rip-offs and cheats. Who knows what else they are doing to your car while they have it? Last time I took one in we got the car back with a couple of foot prints on the dash.