Yes. Each note ends with the line <!-- granite:notes --> and a Notes section. Everything from that line down is yours: it is kept exactly as you wrote it on every sync. Everything above it is generated from Shopify and is replaced when the product changes there; an edit you made above the line stays in the note's version history, and the app's Activity page says it was replaced. To change product copy and send it to Shopify, turn on write-back (Pro and Business).
Granite for Shopify
Can I add my own notes to a product?
Write under the granite:notes line at the end of each note; that part is yours and is never overwritten.