That's because Obama didn't give Chelsea a full pardon.
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.
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.
Now, if Obama has pardoned Assange things might be a little differenct for Manning, but that's a weirder counterfactual assumption.