So I finally took the step and created a prefab for my menu system. In all my scenes I have a menu, where you can press a button on the side and a menu slides into view. There is also another button in that menu that pulls down another panel from the top, where you can choose to jump between chapters/scenes. I had to update some stuff now in it and up until now I have had only made a copy of it and pasted it into all the scenes. It was a hassle doing manually updates for all the scenes so I figured I would try out prefabs so I made the whole menu into one with all subparts.
The first problem was that in the cover scene and another scene, I needed it to be a bit different. So I did changes to it that I didn't apply. But for some changes still was put through to everything.
Then I noticed that when I had made the menu that a FSM I had for changing font size (font+ and font-) had target objects outside of the prefab that it applied the font size changes to. The game objects with the gui text objects on them. When I created the prefab it lost the linking to those object. I then clicked on change prefab in the FSM for the fonts, but it didn't let me add the gui text game objects outside of the prefab. So then I was forced to drag them into the menu and in order for it to stick to the prefab I dragged the menu to the prefab in my project folder. Then all seamed to be working and I did some other sizing changes to some images within the menu and applied it.
I then built for iOS and saved and closed down Unity, was going to bed. I then tried the app and noticed that everything had changed and there was no longer any subtitles at all in the app. So I checked Unity and now the text objects are totally missing from the project all together. Poof, disappeared with all their settings.
What the hell. What is going on?