Thanks to some hints provided in the comments to my original post here, I have been able to locate some sources that answer my questions, at least on a high level:
Beginning in 1989, even before the details of political reunification were being seriously considered, the GDR granted a number of automatic amnesties. Two of these—one on 1 October 1989 and another on 6 December 1989—were targetted at specific classes of crimes, including political crimes like Republikflucht that were not recognized as such in the FRG. At the same time, the GDR also significantly loosened its rules concerning judicial review of sentences and convictions, a circumstance that many prisoners availed themselves of in order to get their sentences reduced or convictions overturned. A third amnesty in 1990, which was made in furtherance of the impending reunification, resulted in a reduction in sentences across the board. Excepted from this amnesty were "Nazi crimes, war crimes, crimes against humanity, murder, and aggravated violent or sexual offences", which were also illegal in the FRG.
Together, these measures had the effect of reducing the prison population from 24,171 in November 1989 to 4375 in July 1990, with still further reductions in the days immediately before reunification. So relatively speaking, there were not all that many prisoners left when reunification took effect, and of these, it's unlikely that many (or even any) of them had been convicted for activities that weren't considered crimes in the FRG.
The third amnesty, the law for which seems to have been carried over into West German law, granted every remaining prisoner the right to have his or her conviction reviewed by an independent commission. These commissions were indeed constituted after reunification, and in about half of all cases the committee recommended clemency, conditional release, or quashing of the conviction.
Nothing I have found indicates that there was any automatic adjustment of the sentences apart from the above-noted amnesties; it seems all prisoners who wanted their sentences altered or convictions overturned had to initiate judicial review themselves, either pre- or post-unification.
I've found this information in various primary and secondary sources, though it's all briefly summarized (with references) in Corrections in the German Democratic Republic: A Field for Research by Jörg Arnold and Johannes Feest (British Journal of Criminology 35(1), 1995, pp. 81–94, DOI: 10.1093/oxfordjournals.bjc.a048490).