How to migrate to SMWSQLStore3 without shell access?
My fault - it seems I wasn't at Special:SMW-Admin when I received the errors in February.
Now I managed to update my database to SMWSQLStore3 :)
I ran the database update twice (as you suggested). Just for curiosity: Why does it need to run two times?
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.