John, great choice for cleaning out your fly box.

I do what you describe basically every year. I clean out my trout boxes ever fall. First I have a small box of flies that I use for the Kansas winter trout season. The best of my left over midges, nymphs, and very small drys go into that "Winter box".
Then, since I have two sets of boxes, one set for trout and one for warmwater fishing, whatever might get bit by a BlueGill or a Crappie replace last years speicimens.

Finally, anything that is left, whether I use it or not, gets given away, stripped, or tossed, and through out the winter I will fill my 4 trout boxes again. I am not the best fly tier, and very much a novice, so each seasons flies are so much better than the last, it makes sence to me to have my best work in the box. Since I enjoy tying anyway, starting over is a yearly occurance.

Ed