Depending on the EC of what you run normally, you may not even need much of a flush. in hydro it's such a short timeframe that it won't have any measurable negative impact on yield or quality.
While i doubt hydro vs a solid substrate would make much of a difference, initial studies show flushing makes difference with the mineral content of the buds. this has to do with biological processes, so it's fairly safe to say that substrate variable is not likely to be relevant. If you run a moderate ppm/ec, i wouldn't worry too much or maybe just halve it in future.. either way the leaves will make up the difference in the short-term.
as far as ata clean.. i'd rather clean it between uses than add anything the plant could uptake -- 'safe' or not. seems like it's a minimum saving in time. can treat the system between use for same effect. unless there's some convenience i am missing.. convenience and personal preferences carry a heavy weight.