If your box is replaced under warranty, Lifetime/All-In service will always be transferred at no cost (even if the warranty replacement was done by a third party, such as Best Buy). However, if TiVo offers a replacement box for an OUT-OF-WARRANTY unit, it has been a total crap shoot on how they handle the lifetime service - sometimes they have done it for free, sometimes they charge a moderate transfer fee, and other times they won't do it at all.
Now that the company has been sold again, I do not think anybody has a clue what we will see in the future.