The encoder should take into account the fact that the decoder will only be working with compressed frames. If it fails to do this, then yes, it may cause artefacts to remain because, as far as it is concerned, no change has taken place or needs to be encoded. sneaker_ger's point is that the MPEG standards don't define how an encoder encodes, they only specify what kind of input the decoder expects to receive, so we can't say what any particular, or all, MPEG encoder(s) may or may not do. There could be other reasons for whatever you're seeing, of course, but since you probably won't provide a sample we may never find out.