I'm with Lewis on this one, everyone in the Tournament obviously has to have the same amount of starting stack, one table versus 13 others with 7,000 suggests that I would favour the option of taking 3k off your players from one tables rather than increasing the chips in play by 360,000.
I don't really see an option that everyone is going to be happy with but to quote mr Spock - "The needs of the many, outweigh the needs of the few or the one" so taking 3k off 1 table is the lesser of 2 or with Lewis's reply 4 different options.
I'm also starting to rack my brains because if this had been a No Limit or Pot Limit event that would make things even harder as some players may not have 3k to surrender! However presumably your tournament clock would have an initial ships or the event would have an advertised starting stack, so therefore it would be the players at the tables responsibility to point out the error.
Best Regards
Stuart