Some queries are starting to come up in the Primathemes support forum this morning regarding Flexishop2 and the Woocommerce plugin 1.6 upgrade. The queries are the same as mine that the product categories and single products all receive 404’s. I rolled back to 1.5.8 and all is as it should be again.
you should probably look into *why*
Being the developer I thought that maybe it was something you could do as well? ??