I could be utterly wrong. but wasn't there a calibre plugin done for this? again I never used it, not even once but I could swear others were chatting about it.
EDIT: Doesn't this pertain to your issue:
Notes on Calibre Synchronization:
Quote:
The Export function exports all collections which contain at least one "normal" item. However, it does not export the collection hierarchy (because Calibre does not support that).
...
Calibre Synchronization will never change the collection hierarchy, or the visibility of existing items. This applies to both import and export.
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As in "No" it doesn't? Perhaps I am not reading that correctly.