No problems here. All you need is to build simple graph like this:
File Source->MPEG Pull Demuxer=>MPEG or MP4 Multiplexer->Sink Filter
Remultiplexing doesn't affect video quality and take several times less time than normal playback. Yes, audio/video synch issues may occur but we haven't heard of such problems for quite a long time already.
Also we plan to make console version of XMuxer (this is expected to happen with version 3.0 release) so any one interested in such tool with out GUI is welcome to try it.