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As @dornhege wrote, you will have to do it manually. Once nodes are created in OctoMap they are assumed to never disappear, i.e., they don't go back to unknown. After an update, you could check the updated nodes (or regularly traverse through all) and then delete the ones that have a log-odds of 0 (or close by).

You could also look at OcTreeStamped (since you mention lowering probabilities after timeouts), and how it is used in collider. It offers you time stamps of the last update.