When you Restore a backup, anything entered in the database since the backup was created WILL be lost. If you create a gedcom of "All", then all the data that was in the file at the time the gedcom was created will still be there when it is imported.
Database software uses pointers as a way of not having to store the same data more than once. Any additional references to that item are in the form of pointers to the actual storage location. As an analogy, in Windows an executable program file such as winword.exe (Word for Windows) exists in only one location on your hard disk, but there can be dozens of shortcuts to it. Likewise, PAF uses shortcuts (pointers) to keep track of what is where.
Occasionally an electrical power fluctuation or other interruption may occur when a pointer is being written or accessed, resulting in a confused pointer. Somehow the gedcom export process seems to be smarter than the Check/Repair process, and can usually fix the problem.