Unlike StackOverflow meta, I've noticed that here all my reputation points have been transferred over from the main. Except for the badges.
Will my reputation be synced between the two? If so, why not the badges as well?
On all meta sites except for MSO, reputation is synced hourly between your main account and your meta account. Since this doesn't happen instantaneously, there is sometimes a discrepancy between the two rep values in between syncs. The other result of this is that votes on meta don't affect your rep.
Badges are not shared between the two sites. You earn badges on meta by participating the same way you do on the main site.