If it has definitely been 3 weeks, you can start bringing up the salinity slowly. You should do it in the course of 4 to 5 days. After about 5 days and the salinity is the SAME as your main tank, you can introduce him into your main tank. If he is still scratching, that might mean there are a few parasites still remaining though, so that has to be your call whether you want to keep him in the QT for a fourth week of hypo just to be safe. This will probably be better for your main tank anyway, since it will ensure that no more eggs will have hatched when you re-introduce your fish. What is the temp of the water in the QT?