I often copy the uncompressed source directly over the compiled file, make my edits on the live file, and then copy it back when I'm ready to check-in. Granted, the system I work with compiles and doesn't concatenate, which is a slightly simpler problem. But you could easily have your build script leave comment markers in the file (or just look for top-level '(function(){...})()' closures which nearly every sane system uses) and "unbuild" the concatenated file from that.