I've partly solved my own problem. Open the old .mov file in QuickTime 10.4 and save it as "Converted." Open the "Converted" file in QuickTime 7 and the sound is back, but not every time. What is really interesting is that QuickTime 10.4 will not open the "Converted" file. Strange.
Again, the problem depends on the audio codecs used and whether or not they are supported. If your system's codec configuration supports the audio codec, then the converted files would probably be playable. Other codecs (like DTS) simply can't be converted using the QT X Modernizer/Convert structures embedded in El Capitan. Either upload a problem file for download and analysis or use a utility like MediaInfo to determine specific problems. If all you want to do is convert the files, then I would recommend using the free HandBrake app. It employs built-in codecs that support most common compression formats and doesn't rely on the QT X El Capitan embedded structures or QT 7 codec configuration for conversion.
