Well, what we know so far for certain is the following:
The derived trait of Charisma is going away.
Multi-Actions will now allow the same action to be done but they are limited to 3 total actions (so you can do 3 total shooting actions, if you wanted, at -4 to each action) I don't see that really affecting Hero Lab, though.
The addition of "core skills" that you get a d4 in for free, specifically Athletics, Common Knowledge, Notice, Persuasion, and Stealth. (Yes, Common Knowledge will be an actual skill now). From that we know there will now be an Athletics and Common Knowledge skill to add to the mix, and I THINK Athletics will be replacing some to consolidate the skills down a bit. That will be something HL will need to work with.
Tests of Will and Cooperative rolls are chaging. The former will be simply "Tests" where you roll any skill that seems appropriate as an opposed roll against that skill's Attribute. An example they use is tripping someone by rolling Athletics and they resist with Agility, since Athletics is an Agility-based skill. This should essentially be what is used in the Flash Gordon rules and also not something that necessarily would need to be tracker in Hero Lab.
Cooperative rolls are how "Support" and you can use any narratively appropriate skill for the roll. So it's no long "everyone trying to knock down the door make a Strength check", but if you can see why Persuasion ("You can do it!") can help the people shoving on that door then that will work. Also something done in Flash Gordon, I think. Again, not necessarily something that needs to be handled by Hero Lab, though, I don' think.
I think there is a bit more on those two in Flash Gordon where some of the rules changes there (including the consolidation of some skills into Athletics) were actually previews on the new "Savage Worlds Adventurer Edition" version (previously called "Savage Worlds Black").