Of course, you're converting these files. So you're basically converting the MP3 to WAV, which doesn't do any harm, but then you're converting it to WMA, which is compressing it. So all the tunes you made into MP3s are gonna sound a bit worse than the rest you just made WMA's out of to begin with.
I agree with Tony, but even if you're main concern is capacity, I'd still recommend re-ripping those songs and encoding them in WMA to begin with. One compression is always better than two.
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Matt