by Guillermo Madero.
Hello Fatema,
Not all zero-sized files should have been deleted, some have a purpose; well, they are history now. At least your PDF are working now.
You could try and just enable the File System repository (even if this seems unrelated):
http://docs.moodle.org/22/en/File_system_repository
You might also want to check the following:
http://docs.moodle.org/22/en/How_to_check_your_database_for_corruption
Cheers!