The role of manuscripts depends on the person doing the psak. There is no hard and fast rule on the subject.
Manuscripts and their role in psak, can be the same as "new" scientific discoveries and thier role in psak. For example, the recent controversy over the anisakis worms in fish.
In general, there are three approaches to old manuscripts.
It's a forgery: Either the manuscript is not a real manuscript, the manuscript is the old opinions of the Rabbi and were discarded, or the manuscript is a mistaken copy, and not real. The copy we currently have, and have been using for generations, is the authentic and correct version.
Wait and see: For us, today, the manuscript has no halachic value. Perhaps it will have halachic value in the future, or large communities and Torah observant people will find value in it, but it is not for us to say.
Baruch Hashem!: Thank Gd we have had the truth revealed to us, and blessed is the generation that merited such a reward. This approach says that we must change our practices right away, and look through all the halachic give and take, using the new information. Perhaps we can solve some machlochet between the Sages, or we can better understand how the halacha came about. Regardless, we must see this as a "bat Kol" and act accordingly.
Lo B'shamayim hee: Same as "Baruch Hashem", except it's argued "lo B'Shaymim hee", the Torah is not in heaven, and halacha does not change based on this new "bat kol".
If one were to split the difference of the many different ways of looking at the manuscripts, you mostly end up with no change in practice, but perhaps changes in the study and the yeshivot. Which may or may not result in a change in practice over time.