It can be done. I have done it. The biggest problem you are potentially going to have is an ammonia issue. If you have a lot of algae, worms, other fauna you are likely going to have a big die off and potential ammonia spike. Therefore, you really need to monitor your ammonia carefully.
The best way I have found in dealing with ammonia is to buy some good live bacteria, like biodigest, and dose it heavily immediatley before and for several days after reaching near or about hypo levels. If you still have any ammonia problems, then have fresh water and/or amquel available. Also, manual removal of decaying algae and/or any other dead organic matter, such as worms, goes a long way to avoiding a major ammonia problem.
I will add that hypo did not work for me in eliminating ich. Now, it is possible (and even likely) that I did not do it long enough and/or maintained a correct salinity level so I am not suggesting it won't work for you. Ultimately, I resorted to cupramining the system thereafter for a full 30 days at .5 which was successful with all fish tolerating the treatment well and absolutely no signs of ich for well over 4 months. All measurable copper has been removed with no observeable negative effects.