Turning trade restrictions in FR/LG off and back on?

[ManaTim]

Hey all, 

So my brother wants us to play through Fire Red and Leaf Green again alongside each other. I just made it to Vermillion City in my copy. However, i'm remembering how much I despise this game's limited Pokedex and all the trade restrictions you have for 90% of it. So, I downloaded PkHex and removed said restricitons so I can trade from another FR save and my Sapphire/Emerald carts. 

Here is my question. I'm somewhat of a newbie and I've heard that messing with these flags can cause issues later in the game. If we trade whatever we need to our copies, and then turn the event flags back off, should the game progress like normal without issues? We both want to do a full playthrough and don't want to run into any bugs that could ruin it for him. If so, would just hacking random encounters to give us what we want be the safer option? 

Appreciate the help!

Edited August 20, 2025 by ManaTim