Jack,
I have been going through a lot of what you have. My sources were a mess. The following has worked for me:
1. Put some kind of typo back into the second source so you can readily distinguish it from the first source.
2. Select "Sources" from the main menu bar.
3. In the top center panel select the first (correct) source-citation. Double click it. In the window that opens select "Copy" in the lower left corner. Close that window.
4. Select the second (incorrect) source-citation in the top center window.
5. In the lower window double click the first link. That should take you to the Person view with the linked fact highlighted.
6. Click the unlink icon in the lower right hand window. That should break the link to the incorrect source.
7. Click the down arrow beside the word "New" in the lower right hand window.
8. Click the last selection "Past Link to Source-Citation" This should link the fact to the correct source-citation.
9. Go back to the Source view and repeat the above from step 4.
10. Keep this up until you have no more facts linked to the incorrect source-citation and then delete it.
It sounds like a lot of work but once you get in the rhythm it goes quickly. Shouldn't take more than 15 to 20 minutes.
Good Luck
George