Are you suggesting the sport got cleaner or they found better ways of masking the doping such as saline IV to dilute the bloodstream etc?
The sport definitely got cleaner. It's just that it didn't necessarily mean that riders weren't doping, instead the biopassport and the advances in anti-doping made from 2006-2008 (which ended as soon as Lance came back and the UCI took over testing again) had meant that the amount of doping that could be got away with had significantly reduced, such that the amount of doping that was required to be competitive in 2009 was significantly lower than it had been in 1996. This is also why anecdotally considered clean riders like Moncoutié and Fedrigo could be more competitive at the time, but not enough to actually contest GCs or anything.
The fact Lance coming back meant the UCI felt they needed to step in and take over testing again, despite the massive number of successes had by AFLD at rooting out dopers in the three intervening years, as well as ASO delivering a parcours which was clearly intended around keeping Lance competitive as long as possible but designed before his comeback so before there was any indication of how competitive he could be (very few decisive mountain stages until deep into the third week, a long TTT which had not been seen since his retirement), tells me there was a vested interest in his comeback being successful - probably because the loss of his star power plus the consecutive doping scandals to hit the race in the period since his retirement had hit audience figures and revenues, plus ASO needed the Tour to be profitable to prop up their loss-making pet project, the Dakar Rally, at the time (this is also why they have branched out a bit and taken more risks the last couple of years, as the Dakar now has an established and profitable home in Saudi Arabia), meant they felt they needed him. He also promised he would publish his data, and then didn't until pressured into doing so by those who remembered he had said that, possibly thinking that in the drama of the Grand Tours and especially with the internal team arguments at Astana that this would be forgotten about (similar to Brailsford's internal investigation into Leinders, which was promised and then swept under the carpet until Dan Benson asked him about it at the World Championships, causing Brailsford to literally run away from the question) - so non-experts who viewed them were overwhelmingly doing so with a skeptical eye, thinking that as he had promised to post them and then had to be coerced into actually doing so, there must be something to hide. And to the layperson, the way the blood values behave differently from the Giro to the Tour and the way they deteriorate before spiking up on rest days sure as hell looks like we would expect from blood doping.
Not enough to secure a conviction, but then after we learned of Levi's 132,8% off-score not being enough to secure a conviction you have to recognise that the margin for error set is pretty huge, which makes you wonder what exactly people like Jonathan Tiernan-Locke and Jaime Rosón must have been doing to trigger biopass positives. And we've also learned that there are huge gaps in the ability of the biopassport to stand up to lawyering up, with the likes of Roman Kreuziger and Daryl Impey poking huge holes in it, securing exonerations for some pretty damning-looking evidence by being able to theorise possible - no matter how implausible - alternative causes. So just because Lance wasn't caught from his biopassport data did not mean that it wasn't suspicious. Certainly not enough to say in and of itself that something was definitively up - there weren't enough clear data points for the amount of longitudinal data required at the time - but the Occam's Razor explanation was blood bags on the rest day and given everything that happened before and since around Lance Armstrong, Johan Bruyneel, Yaroslav Popovych (who had a career renaissance after being woeful with Lotto after his running buddy Volodymyr Bileka got busted for EPO), Chris Horner, Levi Leipheimer, ASO, the UCI and USADA... I don't think there is anything that anybody could say that would convince me that Lance Armstrong rode the 2009 Tour clean or even remotely so. There would have been no reason whatsoever to come back just to be what Chris Froome is to the 2023 péloton, a veteran former champion unable to come close to replicating their past level, waving to the crowd and collecting a paycheck. Lance's ego would not allow for that. If he stood on romance then he'd already had the perfect retirement in 2005, so if he was coming back he was coming back to win, and having done what he had done to do so in the past, and knowing that ASO and UCI likely needed him more than he needed them and had thrown the testing company that had done all that great work over the last few years under the bus...
I honestly think Lance announcing his comeback, and the subsequent (and supposedly connected) UCI wresting control of testing back from AFLD, is probably the worst thing to happen to anti-doping in cycling in the last 20 years. All that progress essentially wiped out overnight.