Yes they can, The original file may be in ROM, but ROM files can be replaced in RAM temporarily, Obviously they will be lost after a hard reset, Copy into the windows directory and SOFT reset so the dll registration entries point to the correct file.

As I knew so far, most of video playback software on ce6 (which is not from the factory of the device itself) is not going to work that good.
just like wmp, coreplayer and etc. is not working well and most is crash and make device freeze.

I think most of software that you guys mention is better use for ce5, but ce6 for me, after wondering around around 1 month, hopeless is the only word I found.