Oh, no, this does sound very serious at the moment! Check his gums (if they are not pink, and instead are grey, then that is sign he is going into shock and it’s an emergency) Do you have any emergency vets?
As far as your other questions –Gi problems are usually a symptom of something, not the main problem, and since there are so many things that can create gi issues, it is impossible for us to know the whys and how it will turn out. When the gi tract gets out of balance it can definitely be what the vet said and bacteria begins to take over causing all sorts of issues. I think every bunny owner has to deal with bunny gi issues at least once, and while most pull out of it with care, it is something to take seriously every time. I have had good endings and bad endings and each time I did the best I could. And sometimes the reason for it remains a mystery, but your vet is right to begin checking further.
I would make sure they check your bunny’s teeth (the back molars especially). Sometimes tooth issues or tooth root infections can cause this.
You and your bunny are in my thoughts this evening — sending healing vibes and hugs your way.