The pardon can restore certain rights in some cases, I'm not entirely familiar with the Stone shenanigans, but knowing the parties involved I can't assume that Stone was legally entitled to do what he did after the pardon, and maybe he was.

That said, the recovery of assets after transfer to Treasury is settled law. [1]

> More broadly, the Court ruled in several cases during this period that pardons entitled their recipients to recover property forfeited or seized on the basis of the underlying offenses, so long as vested third-party rights would not be affected and money had not already been paid into the Treasury (except as authorized by statute).

Was covered in Osborne v. United States, Knote v. United States, In re: Armstrong's Foundry, Cent. R.R. v. Bosworth and Jenkins v. Collard

Subsequent cases make it clear that the offense is not in fact "gone."

> ... the Court in Burdick stated that a pardon “carries an imputation of guilt; acceptance a confession of it."

> ... then, in Carlesi v. New York, the Court determined that a pardoned offense could still be considered “as a circumstance of aggravation” under a state habitual-offender law, reflecting that although a pardon may obviate the punishment for a federal crime, it does not erase the facts associated with the crime or preclude all collateral effects arising from those facts.

The court holds that it is not in fact as if it never happened.

[1] https://www.law.cornell.edu/constitution-conan/article-2/sec...