Having figured out what to do, the protagonist says「これで決定」. Later, having picked one option out of several, she says 「これに決めた」.
What's the difference in the meaning between these, and why are the particles different (で / に)?
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I think these two これs are referring to different things.
In これで決定, これ is referring to the current situation (i.e. what just happened) so a translation would be "and with this/because of this, I have decided". This これ is not talking about what was decided. See this link.
In これに決めた, これ is talking about what was decided. "I decided on this".