So you are saying you have a book that you 100% know you did a calibre conversion on in the past, but shows up as non-replaceable? Have you done any editing on that ePub say in Sigil? It is possible (from what you said in a PM previously) that you have deleted/edited something which means the cover is no longer earmarked in a way calibre understands it?
Fundamentally it is going to come down to one of three things. Either...
(1) there is a bug in the plugin logic and the QC plugin is telling lies,
(2) you haven't actually yet converted/ or run Modify ePubs insert/replace cover feature on that ePub, or
(3) you did run one of those options above, but subsequently edited the epub using Tweak ePub/Sigil and managed to trash the things calibre uses to identify the cover.
If the plugin is telling lies, you can find out for youself by just changing the cover image in calibre and using Save to disk (don't convert/run Modify ePub on it). If the ePub in that output folder now has the new cover, the QC plugin has a bug. If not, then it is (2) or (3) which would be user error
