Have you considered linking notes from one notebook to another? E.g. if you named each notebook and numbered pages, you could just point to "page X in notebook Y", and wouldn't need to transcribe. Would this be something helpful to you?
I run through about two A4 192 page Moleskin notebooks in a year. Every entry is dated, and back references are essentially in the form of “On $date, I wrote ...”, so the lookup is sub-linear time.