Hello,
Currently it is needed to disable the System - Jfrouter plugin in order for JoomSEF to work with JoomFish 2.1.5.
The Update URLs function does not handle that many URLs currently, but if you are using the 3.7.4 or newer version of JoomSEF, you can just Purge the URLs - they will be just moved to Trash (so all other properties, like meta tags and sitemap options will be preserved) and next time when browsing the website, the SEF URLs will be updated to reflect the current JoomSEF's configuration.
Best regards,
ARTIO Support Team