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You should be OK.
The reason this is required is in case a fuel injector leaks, as the entire time you are flashing the PCM the fuel pump is running flat out on vehicles with return-style fuel systems,s which the F-150 used up thru and including the 2003 model year.
Basically, any vehicle that has a return style fuel system should have the fuel pump fuse removed any time the PCM is being flashed to prevent the possibility of an injector leaking fuel and thus filling one (or more) cylinders with fuel, and as a result, bending a connecting rod or having an explosion when you go to start it.
In this case, the vehicle started up just fine, so he got lucky and is OK. Just remember to pull that fuel pump fuse from now on, OK?