Calibre is very good at converting epubs to mobi (and the other way around.) It ships with a commandline tool called `ebook-convert` too so you don't have to mess around in the GUI.
Yes the UX design is very poor, but the core conversion functionality works well once you figure out how the awful GUI works. The `ebook-convert` commandline tool is just fantastic though. It has a very straight forward interface.
ebook-convert input_file output_file [options]
And there isn't very much impedance mismatch between mobi and epub, so the conversion back and forth between the two will almost always be high quality.