I have encountered the same issue after experiencing this with Protected Content BB Codes in @cclaerhout addon. My question to him was, how come after I uninstalled the bb code, then re-installed it, it only shows the text of the bb code and did not actually embed?
This is basically the same issue that happened with Post Replace. So my question is, how can we get posts that were changed or bb codes that were uninstalled then reinstalled, to re-embed the previous posts that had the embed code? What kind of rebuild needs to be done to the message part of xf_post table in order to recognize and embed old bb codes or media links so that it can embed them?