I delete a virtual folder (saved search) within the Search folder. (I want to do this mainly to clear the unread count, also the subject of bugs 295971 and 274936.) I do this by secondary-clicking in the virtual folder and clicking on "Delete Folder" (though sometimes the entry is labelled "Delete Search", which is clearly what's intended to appear always). A popup message says "Are you sure you want to delete the search Last Search? Any messages it shows will still be available in their original folder." I might have named the search something other than the default "Last Search", but the result is the same. When I delete the virtual folder, the enclosing folder called Search (with the binoculars icon) is also deleted. I've only repeated this with a single folder within Search; maybe it's different if there are multiple saved searched. After this has happened, if I do another search with "Body of Message contains" I get a popup message saying "Cannot get search result. Unknown error. (Unable to create persistent search)". Searching with "Subject contains" doesn't give the error. If I stop and start Kontact again, the Search folder is recreated, and search generally works again.
Problem doesn't occur in 4.11.2; closing bug.