I have a similar issue getting the message “Invalid or duplicate SKU” however the error is not related to a duplicate SKU. The issue occurs if I try to update a post with a SKU in the format number-dash-number; example 20339-2. If I change the SKU to contain an alpha character; example A20339-2 the post is updated without throwing the error message.
This is occurring when there is an underlying save_post action.
I suspect that somewhere the SKU is not being explicitly typed as text/string.