hi l_sap120394,
After reading "Command Center" in page35 of the HxFx manual, it looks like it has some degree of programmability:
"Each of its Stomp mode footswitches ... can be used to send a variety of MIDI or External Amp commands to your guitar amps, vintage pedals, synths, or even other modelers."
See if you can assign a fixed MIDI CC number & value to the stomp footswitches you want to use for snapshot changing in Native and then assign the appropriate values for each footswitch.
e.g assign footswitch1 to MIDI CC# 71 and value =1; footswitch3 to MIDI CC#71 also & value=31.
If need be, set min and max value of the stomp footswitch to be the same.
Each snapshot is represented by a value interval of 15
If it works, footswitch1 will select snapshot1 and footswitch2 will select snapshot3.
i suggested using MIDI CC#71 because the manual says that those are not being used/received by HxFx.
Then MIDI learn "snapshot index" in reaper - which you probably did.
I don't own a HxFx but you might want to give it a shot to see if it works.. good luck!