Yes any time the boost pump is on in my RV the indicated fuel flow is about 2 gallons per hour higher, this is obviously a false reading since there is never any change in power, engine sound or air speed.
Are you A, leaning to a fuel flow from the lycoming performance chart? or B, simply pulling the mixture out until the engine starts to run rough and then go slightly richer? If the answer is B then fuel pump on or off will not matter. If answer is A and your flow meter is like mine then there will be a difference.
If you are leaning to a fuel flow then I would switch the boost pump off. Normally the boost pump would be off by the time leaning is done. Leaning in a lycoming should be done any time the power is 75% or less, this has nothing to do with altitude.