Contact the support forum for the GUI that you are using. The behaviour you are seeing is almost certainly due to the way that GUI is coded. Note the “AsteriskNow FreePBX” forum on this board does not provide support for the FreePBX GUI itself, you will need to go to freepbx.org/ for that, if it is the FreePBX GUI.
However, I think this line could be the source of your problems:
exten => 800000031,n(dest-ext),Goto(ivr-3,s,1)
but you can’t change it without also changing ivr-3, and I suspect that is generated by the GUI, and therefore not changeable.
It would be unusual for a file called “extensions_additional.conf” to exist if you had written the whole dialplan.