I think I actually answered my own question here. I turned the above mentioned filter off sitewide and also double checked its turned off on the course too. Course had same setup as mentioned before, Forum and a file resource (a pdf) and the forums description had some html document . I backed up the course, I restored the course and in the new course the forums description correctly points to the new courses resource, not the original backed up courses resource.
so unable to replicate the bug now, but it still persists on our prod
so unable to replicate the bug now, but it still persists on our prod