Understand, I am definitely no expert, maybe one of them will jump in, I hope. I make several wooden baits and seal each one first thing. This is insurance against water gettin' in. My balsa baits get sealed with super glue. My other woods get sealed with Dick Nites. I have found that DN coating really soaks into the wood and provides a good seal without any build up. This is important to me as I make some jointed lures and build up is a real pain in the joints. (no pun intended ). However, I am guessing that you are mainly speaking of re-paints. I would definitely seal the bare wood that shows when hook hangers are removed, paint bait, coat with Dick Nites, replace hardware and go fishing.
Hope this helps
David