[bbatsell]

This is incorrect. Manning’s commutation is just as immutable as a full pardon. Her current incarceration is over supposed contempt of court by refusing to testify in an ongoing grand jury investigation. A pardon for her past conviction would have had zero effect on that. Blame the judge and prosecutors if you think it is contrary to justice.

[somebodythere]

Cheslea can't invoke her fifth amendment right against self-incrimination because she has already been convicted.

If she had been pardoned, that conviction would be null, and her fifth amendment right would apply. She would have a strong legal defence to avoid being thrown in jail.

[akiselev]

That is incorrect. A pardon does not nullify a conviction.

The most relevant ruling would be Burdick v United States (1915) where the Supreme Court majority opinion stated that a pardon "carries an imputation of guilt; acceptance a confession of it." It was an offhand remark which hasn't been litigated in front of the Supreme Court since then so it's an open issue whether the statement above is authoritative and binding but there is zero law or precedent that allows convictions to be nullified by Presidential pardon.

AFAIK only a higher court can nullify a conviction.

[somebodythere]

I stand corrected.