Hi, I'm Dr. Jill. I'd like to ask a couple questions so I can better assist. First, have you noticed any nasal discharge? Second, is there any swelling anywhere else such as his sheath, under his abdomen, or is he stocked up in his legs? Third, has he had his head down a lot recently, and is his feed on the ground or up in a hay net? Lastly, have you taken his temperature, and if so, what is it?
Thank you for the additional information, that is very helpful. My first suspicion would be that the swelling is from a low protein level in his blood. Protein helps hold fluid in our blood vessels (it's too big to pass through normal vessel walls like water can, so it stays in the vessels and attracts water via osmotic forces). However, with inflammation, protein can leak out of larger holes formed in vessels and be dumped into other parts of the body. This is common with colitis and the massive intestinal inflammation (we call it a "protein losing enteropathy" when this happens...or problem with the intestines that causes protein loss). With a low protein, fluid then leaks out into tissues in other areas of the body causing swelling. If he's been sniffing the ground a lot or holding his head down low, this could result in facial swelling. However, we usually see swelling all over the body with this, so it could be something else as well. This problem is easily diagnosed with a blood test to look at total protein and albumin (the type of protein that gets lost) levels. If this is the issue and he's doing otherwise well, we usually watch and wait for levels to come back up. If they're continuing to decrease or they still have diarrhea or are very sick, protein and plasma infusions are good options.
That said, infection is certainly another possibility, including infection with Strangles. His temperature is a bit on the high side (borderline fever), though this could be from residual inflammation with the colitis. Strangles usually causes a prominant nasal discharge, though it may be he hasn't manifested that yet. The swelling you describe above the eyes wouldn't necessarily fit with this though.
You have a couple of options from here in terms of how to best proceed. If he is not in contact with other horses and at a place where he's by himself, you can continue to monitor his temperature twice a day, make sure he's eating well, acting otherwise healthy, and see if his signs progress (general swelling or progression of upper respiratory signs like nasal discharge, bursting open of lymph nodes, etc.) or improve. Horses can shed the bacteria that causes strangles for months without symptoms, so it's certainly possible he was exposed without anyone knowing and his weakened immune system couldn't fight it off. Hopefully this is not the case though.
If he is in a barn with other horses or you have contact with any other horses, I would definitely recommend testing to rule this out. A blood test can look at his white cell and protein levels. Also, there is very fast nasal swab testing available for a wide range of respiratory diseases. It's pcr testing that looks for the dna of viruses and bacteria, and it is highly effective for identifying cases.
This would also look for a variety of other common upper respiratory diseases as well.
Again, we usually see lots of nasal discharge with strangles and other upper respiratory diseases, but it may be he just isn't showing those signs yet. Because of the potential contagious nature of any upper respiratory disease, it's also advisable to make sure anyone going in with him is wearing gloves, stepping in a tub of dilute bleach, and changes clothes before going to any other horses until exactly what is going on is identified. If he's by himself and not with other horses, then this is less of an issue (though changing clothes and boots before leaving to other places with horses and not sharing equipment like brushes would still be important).
I hope this addresses some of your concerns and gives you some options for going forward. I'm glad to hear that at least he's worked though the colic and colitis...sounds like it's been quite a rough road!
If there's anything further I can address to be of assistance, please don't hesitate to ask. I would be happy to continue the conversation and address any additional questions or concerns you may have on this topic.