Cat having issues

Okay, this is really complicated and has been going on over a period of about 4 months now. To provide background and context, I will start with a couple years ago when things really got altered. I had 2 inside cats, brothers. Well, a tragic accident happened and one brother, my emotional support cat passed. His brother, Fluffy, was primarily my daughters cat up to this point and played with her and spent all his time with her and his brother. When his brother passed he became depressed and we became each other's support system and stayed with each other. My daughter got sad her cat wasn't spending much time with her anymore so we got her a new cat. We have had her 2 years now and they have always got along great. He plays with her and they eat together and sleep together and share litterboxes (even when provided their own). Everything has been going good to this point. A couple months ago, my mother in laws health got really bad and when the hospital released her, she moved in with us and brought her Yorkie. And at some point a week or so prior to that we had found, rescued, and removed stray starving kittens. (All of these activities in mid summer brought in fleas) we have been giving regular flea baths and treatments to all our animals and treatments on the house and yard as well and the flea problem has been pretty much resolved. ~MAIN POINT~ Over the last month or two, my boy cat Fluffy has stopped using his litter box, become incredibly reclusive, clawing and chewing at himself constantly, only coming out to eat and pee/poop on floor/furniture. Last week he disappeared for 2 1/2 days and we found him locked inside the spare bathroom hiding in the windows behind the curtain not making any noise or moving. We got him out and he will eat but acts absolutely terrified. I don't know what's going on with him and am so worried. We took him to the vet last month and he had a uti and fleas. We did the medicine and treatments and both issues seem resolved. I'm trying to get him back into the vet this week. We switched his litter when we found out he had a uti to the fresh step health tracking kind (like pretty litter) and have been using that. And got him a calming collar a couple days ago I have a few pictures and a video of his biting/licking, hut can't add them to the thread for some reason.

Hello and thankyou for that interesting and probably very relevant history.  I don't know whether you've gathered this, but one of the main causes of cystitis in cats is social stress.  Cats aren't social animals; they come together to mate and they tolerate others in their territory, but they have strict territorial guidelines within a house.  Fluffy has been very happy in your house with another cat, but recently his territory has been threatened and squeezed, first by kittens, then by an extra human and a Yorkie!  This situation would be a major stressor to any cat, and in Fluffy's case it may have tipped him over from health to cystitis.  Why cystitis?  Urinary sites are incredibly important to cats - they are terribly picky to the point that they will withold urine rather than go in territory that does not feel like their own.  Sometimes they will try to find a new site and thereby urinate inappropriately, which tends to upset owners.  Please be aware that an inability to urinate in a tom-cat can rapidly turn fatal, so if he tries to urinate but can't, or you are not aware of him going, it may be an emergency.  There are things you can do to try to ease the situation; have dog-free places within the house (preferably on Fluffy's natural territory, if you can identify it) and provide lots of litter trays in different places (perhaps with Fluffy's smell already on them), at least some of them hidden from view.  It is advantageous if cats do not have to walk through a dogs' territory to access food and water, for example.  However, ulimately, this is a typical story and it sounds as though the household may no longer be meeting Fluffy's needs (but please confirm this with your vet, who knows the situation better than me).  This may have to lead to difficult decisions.