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There are two ways to lose puppets:

1) A revolution which occurs when a rebel group controls the puppet's capital for a year.

2) A foreign nation puts the puppet in their sphere, which can then have an event that breaks them out of your vassalage.
 
MY question, is what happens when you puppet and sphere a country, and then it ascends to Great Power status? Did you just hold this countries hand and guide it to greatness, only to have to compete with it now?

As France I had South German Federation in my sphere and I built some thing theres, as it helps to keep influence. But it seems this help was enough to push SGF to Great Power status when I removed Morrocco from Spain. I had lost my key ally to fight Prussia...

Lesson taken, always look at positions 7-8 and 9-10-11-12 to be aware of promotion/demotion in the Great Power list.