What making the toilet smell?
If you flush the en suite toilet and get a smell, if you flush it again say 10 minutes later do you still get a smell. As the toilets both use the same soil pipe it does not sound like a sewage blockage further down the line, in any case the water in the loo should act as a barrier to smell coming up from the soil pipe.Check the tank supplying the water to the en suite loo,and see if the water is fresh in it..Where is it fed from, the mains or a cistern in the loft.It almost sounds like a contaminated water supply to this particular loo, which may be exacerbated if it is only rarely used.
