First of all, thanks so much for this mod, its excellent.

Bug: When a blueprint including a compact circuit is updated, further construction of the blueprint will result in the compact circuit building empty.

To recreate: Create a compact circuit with a combinator. Create a blueprint including compact circuit and place in hotbar. Update blueprint by opening it up and clicking the blue icon "select new contents for the blueprint". Build from blueprint. Compact circuit now empty. Doesn't seem to matter whether in packed mode or not.

Now that I know this happens its easy to work around (just always create a new blueprint), but its mildly annoying having to re-name etc. and almost lost a super-complicated circuit (thanks autosave!).
Am I just doing something wrong, or is this a genuine bug?

Your are right, this a bug. But it is caused by a bug in the factorio API.

Technically speaking, the method LuaItemStack.get_blueprint_entity_count() return the right number of entity after a creation. But after an update, it always returns 0, and prevents the update of the entities in the blueprint.

I fear you will have to wait for a fix by the factorio team.

Thanks for the quick reply, good to know!