I am having the same issue, and I have flushed the permalinks (several times). I am working on my site, and every time I add or update a plugin, the wp publications quit working.
Simply visiting the permalinks doesn’t seem to flush them, so the archive works again. If I go to the permalinks and change it to the default, they work fine. Then I change back to my custom structure /%category%/%postname%, sometimes they will work, sometimes not. I may have to repeat this process several times to get it to stick.
I love the archive and the way it looks and works (when it does). Hopefully we can get this fixed so that the permalinks stay put through changes.
Thanks-
Debbie
https://shamanicconnection.com