Like many first users of the organizer, you totally missed the point that it is based on a catalog. Like all kind of catalogs: simple text, spreadsheets or databases, all the information you gather and enter in the catalog is managed within the catalog which includes links to the real location of the media files in your Explorer. A catalog does not store any media file. It only store the path and drive of each file as well as a thumbnail and all your tagging and grouping.
If you move, rename or delete files outside of the organizer, you are destroying the contents of the catalog.
So the number one rule when using the organizer is to never move, rename or delete outside of the organizer (which is built to do that while keeping the links in the catalog updated.
If you (voluntarily or not) move, rename or delete outside of the organizer you have to use the 'reconnect' function where you may be able to guide the search to the new locations. More precisely, that can happen even if you have the same file recorded in two different catalogs: if you move,rename or delete in one catalog, the other catalog totally ignores what you have done in the other.