I came back to Newsblur after some time with the tab closed and now all the missing sites are present at the top level. Could be the same behavior as Moved a folder to top level and it disappeared though as previously noted in my case (a) there was no folder name collision and (b) I tried a hard refresh with no effect so presumably any caching issue was not in the browser.
I also tried adding a new folder with a totally different name and it also had the behavior of displaying all site stories when clicked on, so I guess that wasn’t unique to the name of the disappeared folder but is just what happens when you click on an empty folder?
I’ve gone ahead and moved all the reappeared sites from “Top Level” to a different new folder and most things seem fine. When I find one of the affected sites in Activities again and right-click on the title as before, Change Folders doesn’t error out anymore. I may not have any lingering issues - it may just be the case that moving a nested folder to the top level instead deletes the nested folder and moves its sites to the top level, but in a way that causes them to vanish for a while first?
Also, I don’t know if this is related, but “Import or upload sites” still doesn’t do anything when I click it.