As of 1pm PDT on 20th September, when Mewtwo makes its debut in standard Tier 5 Raids, it will no longer be able to learn the Charged Moves Shadow Ball Ghost or Hyper Beam Normal.
It is strongly advised that you use some Charged TMs before the change happens as Shadow Ball is currently the most useful move that Mewtwo has access to; It will be super effective to the Raid Boss Mewtwo during its outing between September 20th and October 23rd, and will also be super effective to no less than 5 of the Gen IV Legendary Raid bosses.
It is also advised of course, that you ensure some of your Mewtwos have Hyper Beam, if only as collectors items.
If you have plenty of spare Charged TMs, you could also TM Shadow Ball onto any Mewtwo that you’re planning to trade, so that they’re not only more valuable, but also potentially more useful to the recipient.
This will leave Mewtwo with its other two Charged Moves Focus Blast Fighting and Psychic Psychic.
It is speculated at this time that the soon-to-be legacy moves could be replaced by Mewtwo’s signature move, Psystrike, a Psychic type Charged Move which has been in the game code for some time. More details and an analysis on this will be published, if/when it’s confirmed.
Other possible replacements include Psyshock and Futuresight.
Luckily however, the way that Niantic’s announcement was worded suggested that Mewtwo may be able to learn these moves again one day, but only if it is obtained from an EX Raid. Here’s a link to their Tweet so you can see if you’d interpret it the same way.