I don't use fertiliser, but I do use water from my fish tanks (made up of half RO water and half tap) to water my orchids (fairly basic Phals, paphs and catts) which most definintely has nitrates in it as well as other minerals. I dunk them and soak them in the fish water in individual planters/ vases then empty and don't actually flush. I do however try to flush them every coupl of months or so, just in case. So far all of my plants are doing well and seem to like this treatment.
The only thing I would say is that i was slightly confused and possibly misunderstood what you wrote in your post - do you mean that you flush with water/ MSU mixture collecting and reusing this to flush your other plants? if so, then this might cause problems as either disease could be transmitted, or the plants flushed at the end would be receiving more and more concentrated minerals in the water used for the flushing.
I am aware that some orchids are more sensitive than others to the water quality and to the salts and minerals in the medium. Perhaps if you told us what type of orchids you keep, it may help people give a more considered opinion to your question, as what is acceptable for some orchids, may really not suit other types of orchids.
Hope this helps for a start.