Just a few comments...
First, I am really sorry for your loss. Losing a chin is always difficult, let alone two in a short time period. I am glad you have felt comfortable talking to us on the forum, and I hope everyone has been helpful.
As for the vet and her inability to diagnose your chins...that concerns me, and if I were you I would look for someone with more experience with chinchillas. Given a fresh fecal sample, (and I mean fresh right from the chinnie's rear end), a good exotic pet veterinarian will be able to definitively say it's giardia or it's not. The sample has to be tested within two minutes of excretion though or it's no good. It worries me, however, that your vet couldn't say yes or no on that issue. She should have been able to obtain some amount of fecal matter from Storm (I think that is the one you said you had taken to her) and conducted the appropriate test. Also, the $700 cost for treatment of your little guy sounds pretty excessive to me. That is almost what it cost me to have an emergency
c-section done on one of my pregnant mothers.
You did the right thing disinfecting Lollita's cage. I would be careful with bleach though, and not go too crazy with it. The fumes from the bleach can be damaging and possibly fatal for your chinnies, not to mention they are not exactly good for you. A light bleach solution is recommended for cage cleaning, and maybe something only slightly stronger would be appropriate for your situation. I clean my cages with a bleach solution, 1/2 cup of bleach to two gallons of water.
Just some observations and information. Again, I am so sorry for all that you've been through. I hope your remaining chins continue to stay healthy and stable.