Fair enough - it came off like all you said, though, was that it was a "tough encounter," and left it at that.
If there's more to it - such as going into the creatures breath weapon, for example - than there is some leeway for changing things a bit. I also don't see much problem in changing things you would have, anyway, had you a little more prep-time. I for one often run games fairly off the cuff, and as such, I'm certain I've had one or two NPC's who I changed between games simply because I'd been quick to hammer them out initially.
As for the Knowledge (Arcana) check, while I don't believe rewarding meta-gaming should be done, knowing, at the least, that a creature hanging around with a bunch of shadows or near the shadow plane likely has negative energy attacks and is similarly immune to them is one thing they should probably still be granted. The leap of logic isn't too far of one.
Anyway, depending on how much you revealed to them out of game, well, a few changes may not be too far out of line. If you gave them more than "it would have been a tough encounter," while I still might stick to the same encounter, upping a few of the dragons stats might not be so out of line. Keep the same HD, perhaps, but give it better than average hitpoints, abilities, etc.
I'm also fond of giving dragon's spells that are completely antithetical to what they normally are - I believe it was an ice storm that I had one red dragon cast against the players during a one shot I ran. Their spells rarely are the brunt of their power, but having a few surprises is always a good thing, and should be expected of any truly intelligent opponent.
In regards to XP....
I think the players motivation for going back is what's most important in deciding how to reward them. If they're just killing it for the XP, well...how smart is it to go killing dragons just because it might be a "learning experience," eh? I'd penalize the XP for that. I'd up it more depending on their motivation from there - a desire for gold would be a little more, possibly eliminating a major threat to the surrounding area more, and so on, and so on. Seeing as how two separate encounters with the same creature might as well be two separate encounters with two creatures of the exact same type, that two encounters with the same creature should still garner some XP. What might lower it, beyond the potential for just halfwitted PC's who would kill it just for XP, would be their scouting.
Anyway. There's my thoughts. However things go, though, avoid telling the PC's about what's what until long after it matters. You have no idea how much I've been itching to call my player's a bunch of morons for constantly (and I mean constantly) saying that while their characters believe they faced off against a weretiger, the player's know, just know it was a rakshasa. When really, it was just a weretiger...ahh. Sigh. They'll be seeing him again, though. It will be amusing to see their reaction should they actually, in-game, come to believe he's a rakshasa (my players are usually quite good about not meta-gaming), and summarily fire a blessed bolt into him...only for him to sputter a bit, bleed a little, then proceed to turn them into kitty-food.