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I'm going to offer some advice that is provisionally counter to what's been said above about "not changing things".
First of all, "not changing things" is a fuzzy concept in PFS scenarios. You can't change stats/numbers/equipment/feat selections, but you can change basically everything else. It's a well known "exception" to not changing things that you certainly can (and may) alter specified tactics should the players' actions render them ineffective/moot. From the mouth of Mike Brock, you can invent entire encounters such as town guards to deal with players' actions that sensibly require their presence (the party rogue insisted on stealing from a shop keeper, and then got caught..). So, the "don't change things" rule should more accurately be summarized as "don't change things*" with a big ole asterisk.
Continuing on that topic, sanctioned modules are not written for PFS's assumptions about GMs "not changing things*". For example, when I run Master of the Fallen Fortress I include an entirely self-made-up VC briefing stage where the players are told that Balenar has gone missing while exploring the Fallen Fortress and their mission is to rescue him or recover his body, and finish his chronicling of the site. If I don't make such a "change" to the module, the PCs are simple non-pathfinder explorers who by the end of the module are invited to consider joining the society. Nonsense for PFS play where you are mandated to play Pathfinder Field Agents. I'll tell anyone, up to and including PFS brass, that this kind of change fits fairly within the asterisk and is therefore not only fair game, but expected of us to do as a GM meeting our obligation to strive to provide the best play experience for the players.
With regards to The Harrowing, I was also troubled by Biyo's timeline when I prepped the module. I also had to wrap my mind around what would happen if the players simply made him accompany them everywhere... the module seemed to be written with the assumption that the players would just go "thanks info spigot NPC, go along your merry way now!"
I will go ahead and concur with the advice given upthread that making him actively but secretly work against the players isn't a good idea.. but perhaps I'd say so for a different reason. In my view, the module already has a written-in mechanic for the tyrant becoming aware of the PCs' presence via their cumulative successes over several scenes so for THAT reason it's difficult to fit such a change within the asterisk.
As for the ultimate goal of making the dragon more of a challenge... you probably won't need to do anything to "plus him up". Unless the PCs can somehow enter the keep and make it all the way to his observatory without raising any kind of ruckus (about impossible, in my view) his called-out tactics, iirc, are already to be invisible and just roflstomp the party after they enter. With his mage armor buff, SR, immunities, and good saves, the party will be sufficiently challenged to defeat him as-is. The written-in card mechanic is meant to give them the fighting chance.. if they blew it early, then they blew it.
