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OK so in a fresh install of the development branch (9.1.0) from git I created a very simple category import file with the following contents (Note that category id = 2 is "Home" and category id = 1 is "Root" so both are there by default and omitted):

Category ID;Active (0/1);Name *;Parent category;Root category (0/1);Description
3;1;Women;2;0;Clothing for women
4;1;Men;2;0;Clothing for men
5;1;Shoes;3;0;Shoes for women
6;1;Shoes;4;0;Shoes for men

I imported it successfully and have the two top-level categories "Women" and "Men" each with a subcategory of "Shoes". There is the issue however that both the "Shoes" subcategories have their link_rewrite field in the database set to "shoes".

I then tried again (selected options to "Delete all categories before import" and "Force all ID numbers") with the following import file:

Category ID;Active (0/1);Name *;Parent category;Root category (0/1);Description;Rewritten URL
3;1;Women;2;0;Clothing for women;women
4;1;Men;2;0;Clothing for men;men
5;1;Shoes;3;0;Shoes for women;shoes-women
6;1;Shoes;4;0;Shoes for men;shoes-men

This seems to work for me and all of the categories were individually accessible.