You should check the commit that went merged form master to your branch. I know for sure that recently there was something regarding the configuration of the android projects.
Anyway, usually I've 2 different OF folders, one with the current master branch, and one with the current release, in the latter I build the applications. If i want to migrate an app to a newest release, i download the release, i create the new project with the projectGenerator and then I import the files from the project contained in the old release to the new one.
With this workflow I can pull from master without screwing up the apps.