From Atari staff via their Discord on the changes:
PSA Atarians: This is the skinny on Missile Command 🚀 🚀
1. On October 16th, the current iteration of Missile Command: Recharged will be removed from all console stores and the new Missile Command will be available for pre-order. If you want to play the old version, then make sure you purchase it before October 16th. (If you do, you will still get the discount I'm about to mention)
2. Those of you who own the current version of Missile Command will be reached out to and offered a discount on the new game equal to the price you paid for it. This equals out to around 30% off. Full price, the new Missile Command will be $10, so you'll pay like $7.
3. If you have the current version and would like to keep it, you may do so. Even if you delete the old game, you can still redownload it so long as you purchased it before. You don't need to delete the old version to obtain the new version and it won't be removed from your personal library on the 16th or after
4. What's the difference between the versions? New and better visuals, more content, and extra gameplay. It's a very similar game but now brought to the standards of the other Recharged titles
5. There seems to be confusion about the name change and some of the devs just want to clarify that this isn't a "second version" or sequel (even though V2 is a helpful way to discuss it right now before the switch has been made) it is a complete game replacement. The name has been kept the same because the older version will no longer exist except for the people who already have it) and only the Oct. 16 game will be supported in the store and with updates going forward.
This is all the official info, if you heard conflicting information about the discount or anything else, it's incorrect unless it's this ^^^