There's an issue with the current version (1.2.2) accessing source files when the project is re-opened. There's a fix on the way, but in the meantime, the simple workaround is to reset the security credentials before each time you open the project.
Here's how to reset the app's access to your files:
1. Open a Terminal window (you'll find it in Applications > Utilities > Terminal) and type the following:
defaults delete com.drobnik.Linguan
This will delete all your preferences from Linguan, including any references to project folders.
2. Close and re-open your project file in Linguan.
3. Open your project file again.
You'll again be asked to select a folder containing your project files. Ensure that the folder you select is the folder actually containing the source files and resource files, or a parent folder.