Some of those advancements can be incorporated into existing designs, but some can't. Draws to much power, built into the frame itself, etc. So you use the ship until it's next major refit and decide what you want to do with it, keep it going but know it's an obsolete ship, mothballs it or strike it and recycle it to make a new ship.
Lets look at the excellsior, for awhile it was top of the line. But by tng timeframe, its not. It's used as a courier, 2nd contact, cargo runs, follow up explorer, things that are needed but isn't glamorous .. Think lower decks.