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Posts with only deleted children shouldn't show up as having children now. You can still see a post's deleted children if you want to (parent:123 deleted:true).

Deleted posts are indicated in history (the post ID is grayed).

If you've had posts deleted, you'll get a notification the next time you open post/upload. This is mostly because we end up with new users who don't realize their posts keep getting deleted, and just keep uploading low-res stuff until someone gets annoyed enough to mail them to tell them to stop. (I'm not sure post/upload is enough, since people probably often just hit back in the browser to get back there to upload the next post, so it won't reload and show the message; but hopefully it's an improvement.)