Performing this stuff from inside of Civi would be a big win, because it gets rid of the trust and intentionality issues with responding to external information. For example, let's run GET_ORDERSTATUS on questionable charges, which may have been partially processed, and put those transactions into some kind of manual intervention required state. We'll give donor services a button to settle status 600 charges, which will SET_PAYMENT, create the contribution record, and increment the effort_id as usual.
I can't get myself comfortable with doing this totally automatically, cos there's the danger of runaway train charging people's subscriptions due to bugs.
Another possible approach, which makes me a little queasy, is to trust whatever comes in through the nightly audit file, and if the effort ID is equal to or greater than what we think it should be, we increment our effort id counter.