Copying SPs on the website is really easy. It basically has a list of all your SPs, you check the ones you want, and then click transfer and select the destination TiVo. Only the ones you check are copied, so it shouldn't matter how many are on the S3. Although I guess it could effect how quickly the list loads. But it's just once, rather then waiting every time you delete one from the TiVo itself.
Developer for VideoReDo