No - resetting the cutter will not change your print and cut settings. But be sure you have them written down somewhere safe so you can easily put them back in if you ever need to. You don't have to recalibrate the machine once you have the right numbers for you - just enter them in the values and save.
Your print and cut settings are a software setting, not a machine setting. The machine reset just returns it to the default values where it "should" be - all else remains the same.
And as Elizabeth said, check and be sure you don't have a stray node that is telling your machine to do something you don't want. Just happened to me yesterday!