Games you have as owned (marked for trade if you're selling or trading them), games you Had as previously owned if they're already in your BGG collection, games you want to buy as wishlist, and Pre-ordered games as pre-ordered. Never Pledged games, Radar games you don't want to buy, games with no BGG link, plays, notes, prices or loans.
It checks first and shows every change, both ways, before it makes any; skip one and that exact change isn't proposed again. When the two disagree, the newer change wins, and a tie goes to your shelf. Nothing on BGG is ever deleted, and what you set only on BGG, such as a comment or a price there, is kept. A clash, such as a game on your wishlist here that's owned on BGG, is shown to you, never forced.
A game new to your BGG collection goes on with its edition, if you picked one, and the edition you picked is added to a BGG entry that has none. A new wishlist entry goes on at priority 3, Like to have. A game you Had that BGG never had isn't added: BGG isn't told about a game it never knew.
Pre-ordered goes as BGG's pre-ordered flag, which hasn't yet been checked against BGG itself. If BGG doesn't keep it, a later check shows that game still out of step.
One sync makes at most 60 changes on BGG; the rest wait for the next run, and the page says how many are left. On a shared shelf, each person's sync sends only their own copies and the shared ones.