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Update: 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.