I have mentioned this many times, but it has made it into mainstream knowledge

Since I have multiple developer certificates, I always have xcode open in the background. As Stefan said, 2 minutes into EVERY single ios compile, the xcode project edits get wiped. What you need to do is:
1. click on the project name after is it wiped clean (and still compiling in stencyl)
2. do your edits and set the developer field
3. let the project finish compiling in stencyl
You do not have infinite time to make the edits-while-compiling, so make sure you have it set in your mind where you want to click when the wipe happens. I have had to do this for over a year. It is not a new thing.