If the concern is that the wav files are not being deleted because of whatever reason (drive was busy, glitch, etc), why not just manually delete the WAV files that are left over after you've converted everything? Seems a lot easier than going through the process multiple times to get that same result. Search the main folder and subfolders for *.wav and delete them if there are any.
I've also found that, at times, metadata does not immediately appear in the converted (resulting) file. A file rescan of these files fixes it. It's been there for me, just not shown.