Thessia was "lost" insofar as the Reapers successfully invaded it, like Earth. Everyone was particularly upset there because the mission didn't actually succeed and made everything else seems worse.
The Fall of Thessia-Codex, The Reaper War
"The assault on Thessia did not go as smoothly as the Reapers' strikes against other races. While other species met the Reapers head-on, the asari resorted to dangerous hit-and-run tactics to harass their attackers. By engaging in guerilla strategies--blasting a Reaper ship, then jumping to FTL where they could not be tracked--the asari forced the Reapers to remain on the defensive.
Unfortunately, the Reapers' greater numbers allowed them to accept certain losses, so they soon ignored the attacks against them and began orbital bombardment of Thessia. This in turn forced the asari to defend their homeworld with a more traditional stance, facing the Reaper forces directly. As soon as the Reapers landed on Thessia, the harvesting began.
A swift and brutal slaughter of the asari ground forces followed. Resistance from trained biotics barely slowed the attackers down. In the end, Thessia's minimal military forces, combined with unpreparedness in the face of an overwhelming enemy, resulted in the fall of the planet."
Yeah, the Reapers were bombing the entire planet from orbit. Thessia didn't stand a chance. If it makes you feel better, the reason why Humans held out on Earth was because the Reapers were not bombing them from orbit as humans were more important for the harvest. The only group who was shown no mercy but held out were the Turians with the help from the Krogan.
About Javik being canon. I can respect you not viewing him as canon in your game as I most certainly do not consider LOTSB or Liara saving my Shepard as canon. Bioware gave me a chance to skip it, complete with a different telling of how Liara got her Shadow Broker title. But, they still went to that Temple no matter what and those artifacts are still out in the open looking very Prothean like. I'm just sayin'