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I've altered a product form using hook_form_alter, adding two fieldsets in which the first shows some text and hidden input and the second a file upload field, implemented with managed_file.
I'm using hook_uc_add_to_cart_data to manage input from the form. When I only have hidden and text fields everything goes fine (even if the hook is called twice), but when I upload a file the other fields become empty: $form_values does not contain any more custom data, like if it was sent with the ajax file submit.
'Solved' using type file instead of managed_file, for now.