I would recommend changing less water at a time. with a 10 gallon, it is easy enough to do a 25% change. I would only go up to 50% if I knew there was a big problem with the water that needed quick action.
A water change can hurt the tank if:
The ph of the water coming in is quite different, and you do a large water change.
The temperature of the new water is very different, and you do a large water change.
(With a smaller water change, the ph and temp will not change much even if the new water is different)
You forgot to treat the new water with de-chlorinator. If your water supply uses chloromine instead of chlorine - make sure your water treatment product handles that. Chloromine is chlorine plus ammonia. If you only treat the chlorine part, you leave toixc amonia in your water.
When doing your water change, be carefull you filter media does not dry out. This will kill off the bacteria in it. Also, if the filter material is getting clogged, just shake it around and rinse in a bucket of water you just removed from the tank. This will ensure the water you rinse with does not contain chlorine, which could kill the bacteria.
Speaking of filter media, you mentioned a 3 stage filter. The most important to have is the mechanical and biological. The chemical filtration (usually activated carbon) is not normally needed. In fact, you should have taken that out when treating your ick outbreak. Otherwise, the carbon will absorb the medicine. Anway, by rinsing your fitler media as described above, you can make it last much much longer than the manufacturers recommend. Don't forget, they want to sell you more filter parts. If you do feel the need to change the filter material, change oen piece at a time. For example, change the mechanical filtering cartridge, then change the bio part the next week. Some bacteria are on the mechanical part of you filter also. If you throw out both pieces of filter media at the same time, you are basically starting over again with cycling your tank, and can expect ammonia and nitrite to appear in your tank soon.