I like the options David proposed that are tied to both Calibre and Kobo.
Some folk can't upgrade Calibre (OS age, IT Admin rules on those who use a company computer?).
It is just to easy to forget an OVERRIDE was made 'last year', (guilty

) and plug in a newer Kobo (or any brand that uses same device driver), where it IS an issue.
<bias>I hate 'installer' tampering with settings I have made (silently). If they are needed. MAKE Me do (confirm) it.
I would consider allowing a Calibre version Update, to auto adjust the stored Calibre version in the override, IF there was no known critical Device model Driver change needed to avoid NAGs
I think it would just be easier on Kovid and crew, if the message popped similar to the original. (if there is a decision needed)
"<device>" FW update detected. Do you still wish to: <pre-select the previous response) settings
My 2 cents