Yes, you will lose these settings.I'm a complete noob on the FM3 (jumped across after deciding it wasn't worth waiting for the QC!). If I do the Reset System Parameters am I going to lose all the settings I've made (ie - external Footswitches, expression pedals etc)?
You do have a couple of options. If the reset does not resolve the problem you can restore from the backup you just uploaded (and thank you for that!).
You can also export your layouts in case resetting your system parameters does resolve the problem, then import them to restore the layouts, at least. This won't restore other settings, however, just your footswitches.