I had a little trouble myself, but I was kinda lucky. I only had 3 bots total on the server. I just recreated them from scratch and move the botinventory back into the db so they had all their stuff back.
Just committed to SVN a new sql to use that will convert the old style bots and their inventory to the new schema. You can find the file in utils/sql/svn/botsconvert.sql. Use this instead of bots.sql if you wish to convert.
Please be sure to back up your DB before attempting this.
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