The first battle that is in FR from the start of A-Trainer's list is Youngster Ben at battle number 0x59. Every trainer before that is just a placeholder for RSE sprites who only have a level 5 Ekans as a team (No idea why). From Youngster Ben onward all of the trainers are used in FRLG, except the ones without names and 0x1FF - 0x203 which are placeholders for Oak and player characters (Once again, no idea why they're there).
In all my years here I've never explicitly heard of any trainers being dangerous to use, but if I was to take a guess you may be refering to the trainers above number 0x200. Trainerflags are in reality just regular flags in disguise, if you set a trainerflag it will set the trainer number + 0x500. So if I were to beat trainer number 0x23, flag 0x523 will be set. In a lot of documentation around here its stated that flags 0x500 - 0x700 are reserved for trainers, but the fact remains that there are 0x2E6 trainers in FRLG, implying that the last 230 trainers are beyond the safe flags. This seems very odd since those trainers are used in the Sevii Islands/ E4 rematches and I doubt GameFreak would be alright with having over 200 trainers potentially messing up the game. I'd love it if somebody who has dug into the higher trainerflags could clear this up as I've always been a bit confused as to this mismatch between FR's flag documentation and what's actually being used in-game.
Regardless, I don't believe there are any dangerous trainers in FRLG so you should just overwrite the ones you wish to remove. Remember to backup your progress if you're feeling unsure about something.
If you want to know all of the in-game battles so you can filter out the used trainers yourself
here's a list. Just search for the trainer names you want to check.