I saw the under 3 hour version today at the Lyric Theatre. I was at the first two preview performances there in 2018 and haven't seen the show since, so I have no frame of reference on the 3.5 hour version.
The thing that struck me most is absolutely every moment I remember from the two performance show is still there. I know from reading online dream sequences and a Lily Potter Jr plot were cut, but I don't really remember those parts. So from a plot perspective, there was probably a lot of fat to trim.
On the other hand, I enjoyed the watching the 5.5 hour version considerably more, so something was missing from a character development standpoint. The clearest example I can point to is in the long version Albus and Scorpius's interest in each other felt romantic in nature but is not directly addressed. In the shorter version, the relationship came across as more platonic until the two lines at the end, where the script implies they are a couple.