How to migrate to SMWSQLStore3 without shell access?
From semantic-mediawiki.org
Fragment of a discussion from Help talk:Installation
Ouch, I did not notice you post of Feb. 9, 2013 or forgot to answer O_o. Cool that it worked out for you. It would have been really really weird if you were on Special:SMW-Admin and receiving this error. I think that Markus posted to the mailing list on why the refresh has to be done twice. I cannot remember what it was, but it is definitely necessary since to my experience only about two thirds of the job is done in the first run.