Did you rename the Orphaned folder? As a side note, prefixing with a period is not a good habit to be in. In the Finder, this would lead to hidden files. An underscore would be a safer habit to be in.
Your screencap is showing a Tools > Verify & Repair, not a Rebuild Database. They are two separate things. A V&R will not resolve missing files. You need to right-click entries in Window > Log and Reveal or Move to Trash. You would also need to empty the database’s Trash.
An actual Tools > Rebuild Database would enliminate missing files during the export / import / index process.
I deleted the trash and deleted the orphaned files did a rebuild; I did try the rebuild earlier but did not delete the orphaned files to trash nor did I empty the trash.