Where are these Mega Stones? According to the Insurgence Wiki, all the other Mega Stones are available, but the Houndoominite, Reuniclite and Aerodactylite are missing from the game entirely (even though the Houndoominite should be in Rose Crater). Note that I have the either the 1.2.1 or 1.2.2 version of the game (I’m not quite sure which but I think it’s the latter).
They’re not missing from the game so much as they’re just not obtainable during normal playthroughs because of bugs.
So how do I get them?
You wait until a new patch is released which fixes the bugs and makes them available.
Do you know when that will happen? Also I’m afraid of installing a new patch in case it causes me to lose my progress. I’ve already had to restart the game once before.
On windows, your savefile is stored in a different location. There shouldn’t be any risk of you losing your progress.
Just a note, if OP is a mac user, they might have to transfer their save file to the newly downloaded core.
What if I’m not on Windows?
The post above yours explains exactly that; you can transfer your save file manually.