As noted, tag hierarchy is not contained in the .enex export file
However, deleting/restoring notes does not impact the tag hierarchy
Notebook/Tag hierarchy is stored separately from note data in the Evernote database
>>If one tags each note to match its notebook and backs up to enex and backs up (either by notebook or all at once), then after restore one can use tags to reassign to notebooks
That will work
If you tag "each note to match it's notebook", why do you even bother with using notebooks?
Isn't the tag sufficient