To Reproduce:

1. Download the attached project or create any project with two scenes in it, make sure the target platform is iOS.

2. Open scene "testScene_many_models", make sure it is added to the build then goto player settings, select iOS and, for example, change Graphics API to some other setting.

3. Open another scene, a "Scene Has Been Modified" message box is thrown (only if the first scene is included in the build) the Graphics API settings remains scene independent so if you don't save it still remains changed in the new scene.

4. After saving nothing seems to be changed in the scene file itself, when comparing it with the pre-save version using filemerge.

Settings that trigger the message box:
-Graphics API in iOS
-Stripping Level, in Android/iOS/... (it seems to trigger it on scene opened after changing it)

Some other function seems to sometimes tag the scene as unsaved too, but this can be reproduced most consistently by changing Graphics API setting for iOS.