Hrmm. I'm having the same "I repaired HK all the way without exiting the ship and now I'm stuck with a grey HK for the rest of the game" problem.
Long shot, but do you suppose it would be possible to... revert his appearance to the default by removing only certain specific files from the Override folder? I really, really don't want to revert to so many hours back in order to not do it, it would be more than a day's worth of work down the drain
But also looking at drab, grey HK-47 is just depressing.
EDIT: This does appear to have worked; removing the .tga files containing the actual textures for HK-47 from this mod does appear to have reverted HK-47 to his unmodded appearance, so if you make this mistake, and don't want to look at a drab, un-upgraded, grey HK-47 for the rest of the game, removing those .tga files will let you at least revert him to his unmodded appearance.
So basically you have to take it the INSTANT it first appears, otherwise you miss it forever? This was before Leviathan, I finished the conversation then immediately talked to her again, and the option was gone.
Out of curiosity, is the question about Canderous intended to be... missable? I saw it once, but at the time I continued asking about her past instead, but afterward, the option was gone again.