Zygonisias (and other zygos/hybrids, for that matter) are not especially fussy about being repotted. If the plant is in active growth, I would go ahead and do so. I have one that I repotted recently, even though it was sending out spikes. It ended up keeping both the spikes, and the flowers are completely open now. The plant may drop a leaf or two as it adjusts, but it should fill back in very quickly.
If the mix smells rotten, throw it out. There's nothing wrong with letting zygos grow in a mix of bark and perlite; they do just fine in standard mixes. However, since bark is somewhat of a dry medium, you may have to water a bit more often until it retains the moisture.