What happens to a flag when the question in question was deleted by a moderator, and it still says active? Does that mean it was a bad flag or it's just going to sit there?
Normally, flags are automatically dismissed as helpful when a moderator deletes the question.
There is one exception: when the question is deleted automatically because it meets the criteria for automatic deletion or via spam/offensive flags from other users. In that case, your custom flag remains active for a human moderator to review what happened since we don't want to make any assumptions about the content of the flag and its relation to the question.
The question you linked to was not deleted by a moderator, it was deleted due to a sufficient number of spam flags from regular users.
In such cases, any flags other than custom moderator flags will be validated as helpful. Moderator flags will stick around until a moderator actively acts on them, so you can be sure that if you use a custom moderator flag it will always be shown to an actual human moderator.