To be honest, I see the HMs being more closely related to what was brought in from DPPt. There may be a little changes to match that of the originals, but I don't see HM Flash coming back. The reason being is because if it is reverted back from a TM to HM, then that will bring up issues in compatability with DPPt. As well as it being such a simple TM to obtain. Ever since RSE, TM Flash has been buyable in the main Department stores, so like said, I would think they will make it an easy way to get it for when needed. It can work just like how Dig is useable in caves as well, so it shouldn't come to be useless.
As for Whirlpool, I see it possible for it returning as an HM to replace something such as Rock Climb. It'll be a nice touch from the originals and will keep the basic idea of the Whirl Islands actually having whirlpools surrounding the islands. I wouldn't expect every water Pokémon to know it, but basically more than enough may have compatability with it as there are a lot of water type Pokémon to capture. As for removing the whirlpools, that won't make much sense at all. It won't give a purpose to the name of Lugia's location and neither would it contribute to the game in any story matter like before. This conversion of HMs wouldn't be hard to accomplish though as HMs are solid items. They can neither be traded over unless hacked, and there are also only one set of each in the game.