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The question suggests there are two sets of diacritics, one for lowercase and one for
uppercase. When one includes small caps in a font, I think one should use a
third set of diacritics for small caps.
So, in a font that
contains small caps, I use three different sizes of diacritics. An exception to
this, is the special caron that looks like a raised comma. For this, I use the
same one for the lowercase and uppercase (ascender height is usually not very
different from caps height), but a smaller one for the small caps (small caps
are significantly smaller than caps). For the standard caron, I use three
different sizes (from big to small in height): for lowercase, uppercase, and small