Just saw your fix on GitHub, Nice thanks!
did you attempt resaving your permalinks in wordpress?
Yes, but it had no effect for me. Which is why I did a rollback on all my sites to 1.5.8. I have posted a link to this thread in the support forum and asked for volunteers to maybe get in touch with you so you can tack a look at one of the affected sites. 🙂
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? 🙂
