I set up a filter to forward everything from my old google mail account to my new google apps mail. First had it set up to forward everything new and archive - works perfectly, so changed it from archive to delete.

Then set it up to copy everything already there to the new account - couldn't manage it with a filter so just selected everything and forwarded. Then deleted everything once I had checked it worked.

Very odd, but the workaround wasn't too onerous.