Are the tracks actually empty, or are there empty clips on them, without waveform images?
If you're not getting messages of missing audio, I suppose you have the clips on the tracks?
Did you audition the tracks - hear anything? The waveform image creation is a separate thing, the images are not needed to hear the audio.
In case it's just a visual issue (empty clips), emptying the Picture Cache folder makes SONAR redraw the waveform images.
IIRC there is a separate command "Redraw images", too.