Is it an all stainless steel still? If so, it should have been tig welded together and therefore no flux to wash away. My opinion is yes that would be ok. If you are still worried block your offtake pipe with something, throw a couple of table spoons of bi carb soda down the column and follow it with some white vinegar. This with foam up quite explosively so just add the vinegar slowly. Give it a good shake around, empty, rinse well then steam run. (all that info is based on your still being stainless steel, not sure whether vinegar and bicarb is ok for copper).
Cheers, Heffers