Quartus II project included files removed from QSF

[Altera_Forum]

I've recently had two issues where all of my Quartus II included project files are removed from the QSF file. The latest occurence happened after adding a new STP file to the project. I went to recompile the project and was notified that all of the required files were missing. I manually checked the QSF and verified that all of the included files had been removed. However, none of the other settings were lost. This is the second time this has happened however I don't recall what preceded the last time. 

 Has anyone else had this issue? Is there any backup file to recover from? (I have hundreds of include files, manually restoring is a pain and my last backup was several weeks ago)

[Altera_Forum]

If you dont have it in a revision control tool or made a backup manually yourself, then you will have to manually add them again. 

You might be better off copying the lines that include the source files to the project into a .qip file and then just add the .qip file to the project instead, although this will mean you need to control the adding/removing of files via a text editor and not the gui.