However when I try to save the file it tries to convert it to a movie.How do I edit the original file with the changes returning to .m4a format?
Assume you are referring to the data being saved in a MOV container here. If you check the format of the data, you should find it is still in its original encoded format. Basically, some actions (like changing play settings) can be saved using the "Save" file option which saves the changed data in the original container. Other actions (like trimming, pasting, adding tracks, etc.) require the file to be rewritten to reassess the effect of such changes (e.g., file size), flatten the results, etc. and in this case the data will be saved in a new (i.e., MOV) file container. Since Apple's software normally ignores the file extension and checks the internals to properly identify the data type, this is not normally a problem. Some applications, however, do rely on the given file extension and in most cases you can simply change the extension manually back to its original extension without causing problems.
