So am I to understand that those who arrived in US during ban with valid visas in their passports, had them physically stamped cancelled before being deported? 

What will now happen when the Muslim ban is overturned by SCOTUS as unconstitutional? That would seem to mean those cancellations were unlawful, and would have to be reversed automatically upon reapplication. 

Man what a bloody mess! At the least the courts appear to be leaning towards leaving the TRO in places until the substance is decided.