Steps to reproduce:
1. Create a new project in Unity 5.4 or 5.5
2. Change build target to iOS
3. Add a Sprite to the assets
4. Close Unity
5. Open the project on Unity 2017.1
6. Enter build settings windows

Expected result: build target stays iOS
Actual result: build target is switched to Standalone

Reproduced on: 5.4.5p1, 5.5.3p2 (upgrading to 2017.1.0b4)
Did not reproduce on: 5.6.0p4

Note: Unity's Main window name still states it's "iPhone, iPod Touch and iPad" while in 2017.1, but build settings shows standalone as the build target