Are you using a TiVo or a V6? If you're not sure, check here - if you're using a TiVo, then some of your Netflix issues are potentially caused (or at the very least, not helped) by the age of the box's hardware.
Recorded shows - anything that's deleted should be in your "recently deleted" folder at the bottom of the "my shows" views.. unless they weren't actually recorded programmes but bookmarks to On-Demand content? If that's the case, look for "Not currently available" at the bottom of "my shows"
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