I have some phals. I've never tried treating for crown rot and would assume that it's fatal unless new, healthy growth appears. I know people use HPO in aquariums to treat algae but I've not tried it on plants. From a quick search I saw that physan 20 is recommended by some orchid growers so you might be able to use that to attempt saving the whole thing.
If you're lucky, the new shoot might be a keiki, i.e. a new, healthy vegetative shoot. In which case you can gently remove the rotten part, leaving the healthy part. Allow the plant to dry out a little for an hour or two and then dust the whole thing with sulfur powder. Then re-pot (again).
Does your orchid's pot have drainage holes? I have an inner plastic pot with holes and an outer pot with no holes to catch drips and keep the plant upright. Both are semi-transparent allowing light in so the green roots can photosynthesise. I hold the inner pot over the sink once a week and water the roots only, letting it drain through.
Hope that helps.