Yes it is perfectly safe to save the game if you have a Pokémon that has ?35 HP. I've used this glitch with no ill effects whatsoever so I highly doubt you will ruin your game by doing it, as I have done so numerous times with no consequence.
Since ?35 HP is essentially just -1 in HP. If you change a Pokémon with 1 HP to have ?35 HP, they are not stuck with ?35 HP as you can change them back to have positive HP again.
Through the Pomeg Glitch the following can occur:
Negative HP (?35)
Fainted Pokémon in battle
Force an egg to battle
Additional Sources: Marriland and more importantly the video that Marriland has for the Pomeg Glitch on youtube. It explains everything you need to know about the Pomeg Glitch but I'll apologise in advance for the music xD
Hope I helped :)