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If the copy is accurate, it should work... if it changes filenames, sizes, timestamps then it will be considered as a new file. if nothing shows up at all even though it's on there, the card may not be compatible with the kobo.
if in doubt you could power off the kobo entire, make a 1:1 image copy and then resize the filesystem on the new card. kobo will not notice/care about the card switch at all.
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