There have been multiple instances in the last year of feeds disappearing that we assume are related to feed cleanup that’s going on in the background. It has affected me personally 11 months ago and noticed again today. Personally, I have no complaints about duplicate feeds, badly formed URLs, etc. get cleaned up. The problem with this is when the feeds simply disappear with no warning as seems to happen (which I also see you have fixed).
It has been suggested by me in the past that we get the option in the feed options window. Perhaps “mute” the errant site and add the more popular version in the same folder?
The other thing that just occurred to me though would be to apply the same logic you have in the organize sites window to your cleanup. Namely, if you clean up a feed, send a backup OPML via email.
If you have the bug fixed that’s great, this is mostly just a suggestion that could alleviate problems in the future if the bug pops up again.