I should note that this happened exactly one time. I've been trying to replicate it and have had no luck. It might just be an oddity after you load an old save. I'll keep fiddling around.
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I made it happen again! But it's not the second row of locations like I thought, it's actually connected to another issue I reported in a separate comment - the side girls appearing on top of the dialogue box! I think their paper dolls (or whatever) aren't scaling correctly, and I the added height of some of them is what is causing the clock to disappear.
And now that I can replicate it, I should also note that advancing to a new time block does NOT always make the clock return. :/
So getting the clock to decide to show itself again is going nowhere and I can't find a common denominator to why or how it shows itself again. One time headpatting Kana brought it back, but not any other time. One time changing the time block brought it back, but not any other time. One time sleeping brought it back, but not on subsequent attempts. One time talking to Viola brought it back, but not other times.
...maybe it's just shy?