I am suggesting:
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Move the existing structure you have , with all those intertwined things – OUT of the way
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Copy fresh from the old server (Start this task over) into a new “Library” directory
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When the new copy is complete, Fix the permissions.
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Now test it to make certain everything copied correctly.
Example 1 :
Example 2:
Make a ZIP of the source machine “Library” directory".
Copy it to the new machine
Unzip it one directory above “Library”
Move the new folder up/down 1 level if needed.