Well I've spent a fair bit of time looking at the fonts in FontForge and the their decomilation with ttx and I must admit that I'm in way over my head and I'm far outside my area of competence.
The font in question is LinBiolinum_RB. My first attempt was to copy the small cap glyphs from 0xE091 to replace the lowercase glyphs at 0x0061. This worked in that when I embedded the font, it would appear correctly, or at least it did after I removed the lower case ligatures that looked really funny with the surrounding small caps. When I subsetted the fonts, characters (and glyphs) went missing.
I then exported all the glyphs as svg images and created a new font by importing just the basic alphanumeric characters and punctuation. Again they display correctly and again when I subset them, characters are lost.
To check, I used a set of fonts that included small caps (Charis in this case) and everything was fine when I subsetted them. So there is something wrong with what or how I doing this. This is an area that I know nothing about. Any pointers to more information (other that the FontForge documentation, it is good but doesn't tell me the things I need to know) would be appreciated.
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