OK...I figured it out, but I don't understand what it means.
In function load_core_amigacd32, it originally read:
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mute "${CORE_LAUNCH[amigacd32]}"
which resolves to Minimig (and is wrong, because the desired result is AmigaCD32).
It was then changed to:
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mute "${CORE_LAUNCH[minimig]}"
which is even more wrong, because it would obviously resolve to Minimig.
It now reads:
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mute "${CORE_LAUNCH[${nextcore}]}"
which resolves to Minimig, not AmigaCD32.
A working hack is just to change the line to read:
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mute AmigaCD32
but that seems to violate the spirit of the code. I can't seem to work out, however, what variable in MiSTer SAM would correctly resolve to AmigaCD32 (matching /tmp/CORENAME)...in fact, I'm not sure why the value of that file isn't used consistently instead of ${nextcore} as it should theoretically always be correct.