Hey Cjloong...
My deepest condolences towards your dead shrimps.....

From what I can understand from you setup is...Your top tank with shrimps (higher grade?) over flow to the bottom tank (with shrimps too?) then only into the canister filter...So I assume that...The canister is the only filter you have for the setup with 2 tanks? Am I right?

For your situation, first clue that come out of my mind is, big lost of beneficial bacterial, causing bad water quality. But wouldn’t it be funny? I mean, if I’m not mistaken, those 2 tanks are planted, right? But are they heavily planted, with stem plants, or just basic moss kind of tank? That will be another question.

Just my thoughts thou...

Regards,
John