The site that I sent correctly decompresses all achievements bishakl sahihOther sites are showing the same:
https://psnprofiles.com/shkbooot123 (hover over the H icon, says 1,467 hidden)
https://psntrophyleaders.com/user/view/shkbooot123#games (shows 2,200 trophies)
All I can say is that, for others that had a similar issue, making sure the games were not hidden on an actual PS3 or Vita fixed it for them. When you compare your game list vs what you see on PSN, what games are missing? Maybe try hiding and then unhiding the missing games to see if that changes anything.