What is not clear for me is the word 'transfer'.
In the organizer, you can either 'convert' a catalog or 'import' media files.
'Converting' a catalog is relatively fast (should not last for hours) and creates a new catalog without any newer files than the original.
'Importing' may be deceptive because the default option is to scan all your computer and to 'import' (register in the catalog) all media files. Your description makes that likely.
If that is so, your catalog not only has more files than needed, the import was much longer than a conversion, and worse, you have lost albums, stacks, version sets and even tags.
It will be easy to simply delete that bad catalog, but lets start by a real 'conversion' of the old catalog.
In the menu File >> Manage catalogs, you have a 'convert' button. It should show you a list of your catalogs. Select the good one and let the conversion work for you. Ask if something is not clear.
When you have converted the catalog, you can test that you have everything of the old catalog, and nothing more...
Now you can use the menu File >> Manage catalogs to select the bad catalog and click on the 'delete' button.