Para mim, aumentar o CommandTimeout corrigiu o problema.
Exemplo de código:
//time in seconds
int timeOut = 300;
//create command
MySqlCommand myCommand = new MySqlCommand(stringSQL);
//set timeout
myCommand.CommandTimeout = timeOut;
//time in seconds
int timeOut = 300;
//create command
MySqlCommand myCommand = new MySqlCommand(stringSQL);
//set timeout
myCommand.CommandTimeout = timeOut;