As far as keeping track try doing it this way.
Highlight all the songs you want to convert, right click then convert, when done as long as you don't click anything all of the original files will remain highlighted. Then just hit DEL or right click and delete.
If that doesn't work go to View then View Options, this allows you to adjust the sort columns. Using this you should be able to tell the old files from new by using the Date Added and Date Modified buttons. Also helpful might be the file type column, just look at the file types to delete.
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