It’s unfortunately 1). 2) is a bad idea. Because deprecation of a concept usually happens for a strong reason, or because of a duplicate. In the first case you don’t want to continue basing your analysis on it, in the second one updating would not cause a problem.
In order to do 1) we need to build a Cohort Upgrader, which would automatically find all Concepts that are no longer valid and replace them with valid upgrades (for invalid_reason=‘U’). The ones that do not come with a upgrade it would at least list out, so you could do damage control manually, or with the help of the Vocab Team.
That’s what I tried to sell to you in the other post, but you elegantly started a new one - this one. 