After more experimenting, (and finding another article in these forums on the Flexible Content object) I found that I can use the Flexible Content object with a Clone instead.
Now, I have field groups called, “prototype – Zig-zag” and “prototype – Filter Nav” etc as well as “prototype – Filter by Databases” etc so now I can make a new Flexible Content object, and add a clone to that that uses the fields from my prototypes. Now I can modify the “prototype – Filter by Databases” checkbox choices and it will update the checkbox choices in all the other objects where I cloned that field.
tldr; The Repeater object was probably the wrong object for me to use in this use case.
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