OofStatement
There are quite a few issues.
in scene square:
- node Square has the signal visibility_changed() connected to a missing method _on_Square_visibility_changed(). Godot issues an error in the debugger exactly describing the problem.
in scene Gameplay:
in script QuestionZone.gd you declare two signals zoneisGreen and zoneisRed. In the same script you try to emit those signals using names zoneIsGreen and zoneIsRed (uppercase "i" instead of lowercase) so signals are not found. Godot issues "non-existing signal" errors in the debugger specifying which signal names are non-existing.
there are couple more signal connections from Zone node to non-existing methods but I'll let you figure that out yourself from the debugger error messages. They clearly state the problems.
However, all 4 signals you were talking about are in fact connected. You can see this by looking at the signal connections in the inspector/node tab where everything is listed. If connection is listed there then it exists. Note that even though a connection exists the callback function the signal is supposed to call still may be missing (as you can see in the first problem I described above).
What confused you was that little green arrow/door icons were missing in the code editor. That's because you have the same script attached to nodes in different scenes. When you look at the code from within a particular scene it will show you icons only for connections in that scene, i.e. it shows those icons in context of the scene you're currently editing. I suggest you avoid having the same script attached to nodes in different scenes, at least until you get better understanding of how signals operate.
In general your scene structure looks overcomplicated for such a simple logic. Poor scene organization resulted in convoluted signal connections that are hard to follow. You should rethink it and simplify the system.