are we able to run "He" and "no He" in the same batch for different elements?

Yes, you just need to go into the batch screen Tune screen. Right click the tab that says helium and configure tune modes and here you can create new tune modes and set up a no gas tune. I normally just duplicate my existing then change the settings. If you had another batch with no gas you could also import it from File > import from Existing Batch and just check the tune you want from it.

Refer to your Mass Hunter manual for the recommended tuning settings for no gas and make sure the new tune mode has those parameters in place. I like to run no gas first so drag the tune tabs in the order you want.

I would also put Li in no gas unless you are analyzing very high concentrations as any low mass element gets impacted greatly by helium and has so few interferences it’s not an issue.