there is an issue with commerce feeds with this. I didn't have time to patch but for others...here is a suggested workaround.
disable autosku for the product type or types you are importing
run your import
re-enable the autosku for the products
Programatically (I was running imports via an update hook) this is a method for disabling autosku for a given product type:
db_update('commerce_autosku_patterns')->fields(array(
'pattern' => '',
'advanced' => ''
))->condition('product_type', 'machine_name_of_your_product_type'')->execute();
To re-enable run the following (adapting the names to suit)
db_update('commerce_autosku_patterns')->fields(array(
'pattern' => '[your existing autosku pattern]',
'advanced' => 'a:3:{s:15:"update_existing";i:1;s:8:"hide_sku";i:1;s:4:"case";s:8:"original";}'
))->condition('product_type', 'machine_name_of_your_product_type'')->execute();
hope that helps others...
gus