It is not possible to record a track while ‘playing’ a route.
The conversion can be done via a diversion: Export a track as a GPX and mail it to your self or (open it in Dropbox for instance). To do this press open the detail screen of a route and press the Share button (top left button). Select GPX and then Email or Open In… The next step is to open the gpx file and import it back into Pocket Earth.
You could also use another app like Road Bike (runtastic) to start recording your track. You will have to juggle with two apps a little, but it might do the trick for you. (Road Bike keeps tracking your ride in the background while you use PE for the mapping.) Bring some spare batteries…