Thank you so much for playing all five sites and for the detailed feedback! Your guess was right: a few parts (one at Halikarnassos, two at Knidos) were placed under structures and could never be uncovered. v0.11.1 fixes this, so every site can reach 100% and your save carries over. Also good to know: breaking a part is never permanent, the Workshop puzzle restores its quality, and the game now says so when a part breaks. Really glad the slow manual uncovering felt rewarding, that is exactly the feeling I was going for.