From what I have read both are best, as the bacteria causing the rot tend to live in the substrate. Substrate can take a long time to dry out so its probably better to change it out anyway before the problem gets worse.
You can preserve whatever extras you worked hard to get for the enclosure, but the base substrate should go. You can use soap, bleach, h2o2, whatever to clean the enclosure (although if you are preserving mosses etc. that may not help much) if you are sure to thoroughly rinse the chemicals away.
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