Thanks for your quick response User!
I should have provided more information. Most of my files are mobi's converted to epubs or just straight epubs. I guess my question is what is the point of being able to edit metadata or covers if it won't save to a file? Shouldn't a warning pop up and say something like, "you are changing "cover". The epub (or mobi) format does not support editing of metadata".
Calibre is a nice piece of software, but if I cannot save metadata / cover edits, it's utility drops significantly.