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My friend wants to run his, of all things, Imperial Shuttle with a HLC and two mercenary copilots on board.

He says he can either flip the dice that were turned into hits back to crits to use those that were just regular hits into crits.

Is there a specific order these two upgrades would apply?

On the other hand, it is a pretty pricey combo, so I figure, might as well. (I'm not at the game itself, I'll be following a play by play on my tablet. I have 0 skin in the game)

... and I could use it on a B-Wing, too...

Yes, Mercenary Co-Pilot works with HLC.

The text on HLC's card says to immediately change all KABOOM results to BOOM results, which is the first step in modifying the dice results. As soon as you've done that, you're free to use any other ability to modify those dice again (Calculation, Mercenary Co-Pilot, Etahn A'baht's ability, rerolls, etc.).