There are several different "issues/problems" here that need attention, so I am splitting up the quotes, with the possibilities you might want to consider.
... i have had 2 male chins for 3 years and they live together in a big cage with one big rectangular hut where they usually sleep together. they grew up together and get along very well. recently (starting last sunday) my beige chin would stay outside of the hut, while the standard chin would stay inside the hut and not come out.
This could be happening for several different reasons - a struggle for dominance, OR you may have a male and a female instead of two males {turn them over and compare},please. If they are different, you have one of each and the female may be, or may soon to be, pregnant you will need to get/make a chin-kit-safe-cage a.s.a.p. If one of the chins is a female. If they are of opposite sex, but born to the same parents ... incest is not good ... I would separate them.
... unusual bloating near his male organ, which ive never seen before. i am not sure why... but does chin look like that only when theyre pregnant...? it cant be right... im pretty sure he is a male, or at least i can tell from his organ.
"Pretty sure" is not a positive ... I would want to be positive about both of them being males, over not being positive, and finding dead kits in the floor because the wire is to large to be safe for little kits.
Male chins, like most males in the animal kingdom, do not get pregnant ... that is a task, that is to hard for them, or/and we would have -0- population growth, so God assigned that task to the female of the species.
Sorry, guys, that one was just to tempting and easy to leave it out.
so i immediately isolated him into the upper level of the big cage (i have 2 levels
Transferring one to the upper level of the cage is not truly separating them. The one above can pee and poop on the one below ... AND ... the one below can bite toes, feet and the tail of the one above it ... Contuning to keep it stressed out.
... whenever the beige chin tries to go in the standard chin would make this noise signaling its annoyed and attempt to push away the beige chin.
Chins often need their personal space, just like humans.
OR, there may not be enough room for both chins inside the hut - one could be over heating the other.
OR, there could be a dominance issue, which can become quite dangerous, should they get into a serious fight. A serious fight includes, but is not limited to, blood and broken skin from bites. {sometimes even the death of one or both}
OR they are not both males, but are actually one female and one male and the female is going into, or coming out of, season and is in no mood to accept the male's advances.
sometimes the beige chin would force the the standard chin to get out, but then they end up chasing each other violently around the cage (which usually happens once per day or two, but this time whenever they see each other).
This could be just playing OR it could be a warning of what is to come, but often can be much worse. I would check both at least once a day ... any signs of blood, I would separate them and never let them back in the same cage again ... my personal opinion (not always shared by others).
..the standard chin seems to be afraid to even come out to eat or drink water.
This is never good ... one can, and have been known to, starve the other to death ... I would definitely separate them into separate cages, if they were mine.
... so i took the standard chin out to take a look, i was wearing a t-shirt and when i hold him to my arms, his worn-out fur was all over my t-shirt. normally he doesnt lose that much fur, but this time its alot.
A loss of that much fur could have several problems: stress, over-heating, diet or health issues. Chinchillas are known for their ability to "shed/slip" their fur in an emergency situation or when frightened. Can you take a picture an post it or could you just send me a picture if. (Prey are often left with nothing but a mouth full of fur.)
i checked his belly and bottoms, and the fur in that area is particularly wet, and i see this unusual bloating near his male organ, which ive never seen before. i am not sure why...
First, I would make sure he is a he and not a she.
but does chin look like that only when theyre pregnant...? it cant be right... im pretty sure he is a male, or at least i can tell from his organ.
Male chinchillas do not get pregnate.
...so i immediately isolated him into the upper level of the big cage (i have 2 levels, you know the very big cages for ferrets), gave him water and food. when hes alone in the top level he seems really happy, started eating, drinking, etc. right now they are isolated and things are peaceful, and theyre just sleeping now.
In a two level cage, the chins are only 1 wire apart ... one that can be easily passed through ... toes and tails will be bitten by the chin in the cage below, and will keep the shy one in constant fear. This is not a true isolation or separation, and would leave the one in the top in fear, and the one on the bottom in constant need of a bath.
i tried to put them together again... but it got worse, when i put the beige next to my standard, the beige immediately starts humping him, and now the standard became very scared... i have to separate them again, but even if hes staying by himself, hes becoming less active, eating less and drinking less
Fear of being returned to the same cage/stressful situation with his former cage mate may still be having a stressful effect on him. At this point, from what you are saying, he is constantly in fear of this because you keep trying put them back together, not to mention they are only a wire apart ... a wire barrier that is easily passed through. I would not do this, not even during playtime. I would give him lots of TLC and extra attention. Chins do not tend to get over things (emotionally and physically) as quickly as most animals do. There may have already been to much stress. What do his poops look like? soft & moist, but not sticky wet? or smaller and dryer than normal? Number of poops as compaired to the other chin's amount? more or less?
Personally, I think it would be well worth the price of a second cage, to avoid future possible injuries to the second chinchilla. Vet visits are not cheap.
Jo Ann