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Importing using the application called Store Manager for Magento it is possible to assign product to multiple categories of different depth.
Using your example, to assign product to 3 categories Baloons, Latex balloons and Colored, in your .csv file you need to indicate 3 category paths separated by double delimiter (I use pipe symbol - |):
Novelties|Balloons|Latex Balloons|Coloured||Novelties|Balloons|Latex Balloons||Novelties|Balloons
each double pipe || means end of 1 category path and beginning of other one.
In case your products are in your database, you can update categories in bulk using \"Assign Categories\” option of Store Manager for Magento. There you need to check parent categories, and Store Manager will apply them in bulk to all selected products.
In any case, you can try out this solution, as there is 2-weeks free test version of Store manager application -
Let me know if you need my assistance.