On the Linux machine,
- Settings - Server - Library
a. Turn off Automatic update
b. Turn off Empty Trash - For each library section - EDIT the section
a. Add the new directories
b. Do NOT delete the old Windows paths yet. (this preserves your metadata)
c. Save the changes to that edit
d. Scan files for that section
e. Observe the numbert 2 displayed for each item as it’s found.
f. When all media found (all show the 2)
g. EDIT the section again
h. Remove the Windows path(s)
i. Scan files again
j. Watch the “2” disappear
k. When all files are free of the “2”, “Empty Trash”
l. “Clean Bundles”
m. Proceed to the next Library section. - When complete:
a. Enable Empty Trash
b. Enable Automatic scan / detect
c. Perform full scan one final time
d. Optimize database
The above is from memory.
This is the same procedure, fully detailed once the host has been cloned (which is what occurred here)