Can't make a backup after changing directory structure

Question

Having finally seen the obvious light about restoring a backup I've found some of my directories to be messed up. Some a little and others a bunch.
My first objective is to get a directory and its sub-directoried to agree as far as total file count is concerned and I'm not getting there. I have a directory the shows a total of 1082 files. When I totaled the number of files in the sub-directories I had 1080 files. I found two files that did not belong in the directory. I removed the tags from the two files (pictures) and then removed them from the catalog but not from the hard disk. They belong to a different catalog. When I totaled the sub-directories I got 1080 which meant the two files were gone from the sub-directories. But, the directory total was still 1082 and noted that two files were not shown. WHY? If they arn't in the sub-directories why are they counted in the main directory?
If you can't check your directories this way what other way is there?

Answer 1

Just a note to say that I never owned version 3 of PSE : PSE2 (long gone...) then PSE4, 5,6, 10, 11.
Minocq wrote:
Can I open a new catalog and import these files without loosing these links? Or is the linking a part of the data attached to the files place in the catalog data base and will be lost on importing to the new catalog?
Very important : a catalog is like a list where information read from the files are kept : dates, file size, exif data. Then you can add many info for those files : ratings, tags, captions, notes to that list . The catalog does not contain picture files : it only stores the location (path) of each file.
So, when you create a new empty catalog and 'get' media files, you are only reading your media files to extract the relevant information to be stored in the catalog (a database). Reading those files does not change anything.
When you add information in your catalog, generally nothing is written automatically into the files themselves ; however you can use the file menu to 'write metadata to files' voluntarily.
Now, if you have a catalog with already many pieces of information recorded, what will happen if you start a new catalog ? The new catalog will import all the information present in the files. The original info like exif data, plus the info you have specially 'Written to files' as stated above.
In your PSE8 version, you can work in folder view or in thumbnail view. When you have added a lot of tags, categories, ratings, captions, notes, folder view is not necessary. However, folder view enables you to take advantage of your folder organization with significant subfolder names to quickly add tags to whole subfolders at a time. It's a good way to enrich your catalog. If you still rely only on folder view to organize your categories, that is possible in the Organizer, but relying on categories, tags and albums while forgetting about folders, is the philosophy of the Organizer and its real power.
The main rule is to keep only a main catalog. Have you already tried to import most of your files in your current catalog ? How many pictures are shown ?