How to reproduce:

1. Open any (new) project
2. Build to iOS
- Make sure to select a folder that is not the project root, nor is inside the project folder
3. Build to iOS again, to the same folder
- Note the warning: "Build folder already exists and was created with other Unity iPhone version or for different target device setting. Would you like to replace it?"
- The workaround is either to build into the project folder or to replace the build every time.