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Doesn't the instructions on the bottle say to wait until you're low on gas?? I'm pretty sure it's that way to increase the concentration of the Techron that the injectors see. Since the gunk would be at the injectors, and the gunk would just shoot into the cylinders and get burned up, I don't think the fuel filter is at risk.
I had the injectors cleaned with a little top end cleaner & gas put in a cannister under pressure at the dealer while the engine was running , but was disconnected from the cars fuel system, so the injectors were cleaned & flushed, and basically as new again..
I've been having sending unit issues over the years, so Techron was recommended once a year.. Not sure how much cleaning actually occurs in the tanks.. I guess that was my only concern..
Anyway, as often as I'm in for an oil change, I can change out the fuel filter if needed.. Was just looking for opinions..from guys who have been doing the Techron thing..