Upgrading from Drupal 4.6 has always been complicated by issues of character sets, but the Drupal upgrade scripts normally solve most of these problems for us. But when your dealing with a complex upgrade you need a good understanding of how Drupal is dealing with character sets in Mysql. It all comes down to this - pre 4.7 Drupal stores utf8 encoded data in latin1 based tables (although this sounds a bit silly there were...
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