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I never bother holding onto installers, msizap will do the trick on the rarest of times you hit this situation. As to how it happens, is it not the case that if you run some kind of disk cleanup utility with an aggressive setting that it will purge the windows copy of the installer, and that is what causes the issue?
And in case there was any misunderstandings above, it is nothing to do with calibre that an install process requires uninstalling the previous version using the previous installer copy that windows secrets away. That is just how the msi installer process works in windows for all applications, not specific to calibre. That you are being prompted from a missing installer file means something about your windows setup has been screwed up IMHO.
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