I can’t seem to replicate this issue anymore and thus closed out the bug I submitted below. I ran into an issue this morning after disabling comments site-wide on this particular site that I could no longer enable the Discussion widget to disable comments on existing posts. Since this seems like an issue others would run into, I took the liberty of creating a bug against WordPress 4.1 addressing the issue
. If you’re interesting in following, feel free to do so here or via the bug itself.
While clunky, my work around was to re-enable comments site-wide so as to have the Discussion widget return as an option in the Post Editor so I could disable comments for my existing posts. I cannot speak as to wether it was limited to just published posts as I did not test it.