Mage_ImportExport_Model_Import_Entity_Product::_saveCustomOptions the custom option type "file" is commented out in product import. If you uncomment it and change
'image_size_x' => 0, to
'image_size_x' => null, and
'image_size_y' => 0, to
'image_size_y' => null, below (following http://www.magentocommerce.com/boards/viewthread/275362/), you can reenable it. I just tested it successfully and was able to import custom options of type "file".
Does anyone know why this isn't enabled by default?