Agree with Tiffany, a repot is okay. What media did you use before? My epis are using bark mix,some coco husk chips ,clay rocks and pumice, so it remains airy and porous.
I also get some softened padsin some of my Epis, and I notice it occurs on mine when we suddenly get a cold dip in temps, part of the pad goes yellow and dries out. Once it goes brown and brittle I just tear that part off, by then the plant has properly callused itself.