I would say that the question of the nature and composition of the Shivan fleet in FS1 is resolved
because of FS2's new information, not in spite of it. In other words, we're given the answer in no uncertain terms based on what we learn in FS2.
Think of the Knossos in Gamma Draconis. It was seemingly deactivated by the Ancients in a (vain) attempt to stop the Shivan advance, and it wasn't activated again until the Trinity did so on Bosch's orders. That's a good 8000-year span without any contact between the GTVA's current area of space and the systems beyond Gamma Draconis. From what we see in Into the Lion's Den, either the Shivans' core space itself or at least some large concentration of them lies beyond that series of Knossos portals; one can even surmise that creating them and stabilizing those nodes is what brought the Ancients into contact with the Shivans in the first place. Since we know all of that, is it any real stretch to assume that the Lucifer fleet is the same fleet which destroyed the core remnants of the Ancients' empire 8000 years ago?
The Vasudan scientists stranded on Altair recognized the planet as having been attacked by Shivan weapons; since the Lucifer fleet's weapons were the only ones they had any knowledge of, it's no stretch to assume that the Lucifer itself caused the destruction. Let's say that, after wiping out the Ancients, the Shivan fleet returns to Gamma Draconis, only to find the node sealed behind them. Cut off from whatever command structures the Shivans possess, the Lucifer and her accompanying ships have no other choice but to find someplace to sit around and wait. Fast-forward 8000 years, and they begin to pick up signals from two other subspace-capable species that are currently going at each other...and you know the rest.
So there you go. That's all based on information that we learn in both games, and it easily explains why the Shivan cruisers and destroyers in FS1 don't possess any sort of beam weaponry. No retcons required.
Had the GTVA been surprised of the beams then Petrarch would have mentioned them. The fact that Petrarch didn't is a clear evidence of retconning because retconning, as I said, means changing stuff and pretend that it has always been that way. There was no need to mention the presence of beams just as sure as there was no need to mention the fact that most Shivan ships are red.
Petrarch didn't even need to specifically mention the fact, since anyone with a pair of eyes could see the sensor video clip in that command briefing showing a Shivan ship firing beam cannons. It was an established fact at that point. Just because he didn't express surprise in that one briefing doesn't mean that the GTVA as a whole didn't express surprise when the information was first discovered. Just because the game didn't explicitly state a certain reaction or stance doesn't make that stance any less feasible.
Or maybe it was all some nebulous retcon to work around the fact that
had managed to put spiffy new weapons into the sequel. But if that's the case...who cares?