pokemon-omega-ruby-alpha-sapphire
Can you reset Pokémon and keep all your Pokémon you may have moved into another game? For instance, if you put all your Pokémon from ORAS into XY, can it still delete all of your Pokémon even if they're in another game?
What would happen to my Pokémon in other games if I reset ORAS?
The mirage tower is definitely not present in ORAS. The fossils are just laying on the sand in the desert on route 111. An observation that points to this fact.
Also from Bulbapedia -
A Backpacker in Pokémon Black and White 2 makes reference to the tower, saying, "The Mirage Tower in a desert of the Hoenn region has disappeared."
According to Serebii and Reddit, You DO get something for having a RSE pokemon travel back with you to ORAS Hoenn, you should get a certificate like this:
How to obtain it:
Go to the Cove Lily hotel in Lilicove City, on the second floor you'll see a guy wearing a dinosaur pants walking around a table, he is the director of Gamefreak, talk to him and show him a pokemon from R/S/E... and there you go.
Source: Gamefaqs
Best Answer
No. You would not lose your Pokémon if you transfered them to another game.
Since the other game (in your case, X/Y) has no idea that the OR/AS game has been reset, it cannot destroy the pokémon.
Even if it could somehow contact the other game and delete the pokémon, this would provide grief for those on the receiving end of trades as they would lose pokémon (because some random person they traded with reset their game). Hence this feature is left out intentionally.