When a jelly receives a great answer, and it becomes flagged and removed, does the jelly still hang on to those great answer points?

Only the really good ones – but not the great ones. Those go to the mod.

Only when that happens to me.

Yes

I think they go into the jelly pool.

I sometimes, maybe more than sometimes, go off-topic in the General section.
But. I assure you, I really have no alterior motives; I am not attempting to do anything like “accumulate some funny great answers instead of actually putting forth a quality investigative answer,” I either forget that I am answering a question in general or I just can’t help myself; I just can’t help being a smart ass sometimes.