Hi:
Like you, I migrated my music library from C: to D:. I did this outside of MC. This was purely a wholesale drag-and-drop COPY operation inside Windows Explorer with the two drives, C: and D:. I was careful to preserve the C: data until I was sure the D: data was valid. At the conclusion of the copy operation, I changed the folders to watch (Tools > Options > Library & Folders >Auto-Import > Configure auto-import...) to point to the new music folders on the D: drive and then retagged the Filename fields with the 'Find & Replace' WITHIN Rename, Move, & Copy Files option. I changed the path prefix from C:\... to D:\.... That was the extent of the migration.
This approach preserved the integrity of the sub-folder order (D:\flac\[Artist]\[Album]. Which option within MC's Rename, Move, & Copy Files option did you choose? If you have preserved your C: drive data, I'm sure I can help you migrate your music library to the D: drive.
Cheers,
Lawrence