are you referring to a boiler, either producing steam or hot water for heat, and domestic hot water?
send us the make and model, along with some pictures. some boilers do not need a flue up to the roof, while others do, so that flue location may be the key.--nbc
To move everything. You have to move duct work or piping, flue, gas line, electric ect. Flue length has limitations. Or you have to by new equipment that is direct vented. better off working around it.