Yes, do the upgrade. The upgrade is for fx coin to the newer address (0x), it doesn’t and shouldn’t affect your PundiX tokens.
Scroll further down on the new upgraded wallet to see pundix chain. You should see your holdings there.
Or maybe actually you may need to switch your address on your pundix chain. Simply to access this, tap the pundix logo (or the three dots next to the logo on the right) on the wallet to see any other addresses you have on PundixChain and your holdings should be there.
Also copy your address into the explorer to verify.