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I am a new firered rom hacker and I can't seem to understand which flags are safe to use and which aren't. People say using 0x1200 and above are safe but I don't understand it
The ones labelled unused are safe, obviously.
The story flags and hidden item flags are used for those events. If you've removed those original events from your game or plan to, so you don't mind them breaking, you're free to use those too.
Don't mess with the system flags unless you know what you're doing.
Really curious where you got that info. Those flags are definitely not safe to use in vanilla Fire Red if you don't know what you're doing. I see plenty of people using those lately?