R.java is quite different in Android Studio than it is in Eclipse. Since you say this is an old project, I'm assuming that it was originally from Eclipse. In Eclipse, R.java is included in the source tree. However, in Android Studio, it is hidden away. From another Stack Overflow answer:
1. build
This has all the complete output of the make process i.e. classes.dex, compiled classes and resources, etc.
In the Android Studio GUI, only a few folders are shown. The important
  part is that your R.java is found here under
  build/source/<flavor>/r/<build type(optional)>/<package>/R.java
You shouldn't need to manually interact with R.java at all. It can be re-generated from the source code. Thus, it is likely that you won't have any problems -- R.java will be auto-generated and all will be well. If it isn't, try a rebuild of the project.