Today, whopping tre times I'm have need to setup the Xcode again, because glbasic dedicated to replace project.pbxproj with the glbasic default one. Its very annoying when that happens, because im have a lots of extra files in the project.
So this is a major bug and im hope its can been fixed, so project.pbxproj does NOT got overwrote when that file exists (so do backup of that file often).
So in the next beta im hope there exist a option, so its only copy the xcode project files if not exists in the project options. The same could also go for the Android tempateproj folder (howover you do have more control there).
PS. Sorry if im sound negative, im was very tired when its was happens while trying to implement inapp purchases for iOS (which was in near goal).