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Make an event at that spot that will turn on a switch that prevents Pokémon from being caught, start the encounter and turns the switch back off afterwards. This is similar to programming an encounter with a shiny legendary Pokémon. Its trigger will be player touch. You will need to use a self switch if this encounter is a one-off.
Programming the uncatchable Pokémon script is as follows: in PokeBattle_Battle, def pbThrowPokeBall(idxPokemon,ball,rareness=nil), add the following code below the def line:
Code:
if $game_switches[nnn] # change nnn to a switch you're not using
pbDisplay(_INTL("It dodged the thrown ball! This Pokémon can't be caught!"))
return
end
This is derived from Desbrina's Lavender Town Ghost tutorial found in the wiki.