sure you can do that with JRiver ... from main menu Tools=>Advanced Tools=>Convert format. Select the files first of course
If you want to do this before importing, use the internal "explorer" under Drives and Devices in the Tree on the left of your screen (have to uncheck to view files not imported to library).
Make sure you configure the options first
(you could set the path for one that is already watched in your auto-import setting too)