Healthy water is key to providing them the optimum chance of recovery from all kinds of issues. Some resolve on their own in good water, others need our intervention.
It's important to make sure your filters are clean, a low organic load in the pond and so forth.
Back to the health issue, I'm glad you did the scope. It is good to rule out parasites, if possible.
At the first sign of redness (beginning of hole/ulcer), if it does not seem to be improving, it is necessary to pull the koi, sedate and at least topically treat it. With your Ogon, it appears as if the infection was starting on the inside. Without injectable antibiotics, that can be challenging. There are dip/bath medications that you can purchase and I would advise you have them on hand for future use. Sometimes you can do a group buy in a koi club for medications. I use Oxolinic acid for some qt protocol and it's good for a number of bacterial issues.
https://www.koiphen.com/forums/showth...ive-Discussion
Hexamita is called "Hole in the head" disease. I've never had it but others may be able to see if they think this may have been the issue.
It's important to be able to at least treat topically and the above link has a list of products to have on hand for use. Iodine, neosporin and a sedation method can do a lot for topical issues.