I see couple things that may be contributing to your problem. In the script starting in line 14 (I renamed it to @done for clarity), you have the set flag as an unsafe flag. I added a zero to make it flag 110, instead of 11. Another problem is that when you set the flag, you need to do it AFTER you use the "disappear" command. Also, you will need to set two flags, since two sprites are disappearing. It should look something like this. (The changed part is underlined).
#org @done
'-----------------------------------
message @pass ' You beat him?\nYou a...
callstd MSG_LOCK ' Built-in lock command
fadescreen FADEOUT_BLACK
disappear 0x5
disappear 0x4
setflag 0x110
setflag 0x111
fadescreen FADEIN_BLACK
release
end
#org @pass
= You beat him?\nYou are ready.\pWe fight the Nidos.\nWe're a resistance of sorts.\pPerhaps we will meet again.
The person ID numbers in Advance map should match the flags you set, and the person event numbers should match the numbers used in the "disappear" command. Hopefully this works.
#org @done
'-----------------------------------
message @pass ' You beat him?\nYou a...
callstd MSG_LOCK ' Built-in lock command
fadescreen FADEOUT_BLACK
disappear 0x5
disappear 0x4
setflag 0x110
setflag 0x111
fadescreen FADEIN_BLACK
release
end
#org @pass
= You beat him?\nYou are ready.\pWe fight the Nidos.\nWe're a resistance of sorts.\pPerhaps we will meet again.
The person ID numbers in Advance map should match the flags you set, and the person event numbers should match the numbers used in the "disappear" command. Hopefully this works.