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 @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.
I haven't worked on it at all recently because I have been busy with life in general. There are lots of other things in life that are more important than hacking hobby, but when I have more time and will, I will get back to it. But yeah - haven't done anything with it for a while.