Does freezing sap freshness? Will acids bring the flavor back?
Freezing will not reduce acid.   Chemical reactions tend to slow down when at freezer temperatures, not speed up.

Fresh flavor is a complex amalgam of many factors:  texture, aromatics, color, and so forth.   While acid is perceived as lending a brightness, it is not the only factor in freshness.  After all, your sherry vinegar is far from fresh, but quite acidic.

While there may have been something off in your stored portion that was masked by adding additional vinegar, it is almost certainly not related to having frozen a portion of the soup.