Using the definite article means that the speaker is referring to specific notes already mentioned or known.
It's possible to drop the definite article when referring to notes in general.
In notes taken at the time of the accident, ...
From notes found in her journal, ...
In notes from around the globe, ...
In notes he gave me, ... (not any notes in particular, but notes in general)
In the notes he gave me, ... (a specific set of notes, as opposed to other notes he may have written)
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