They're used more in Pathfinder Society Scenarios. Pirate Ship shows up in Skull and Shackles and the Outpost mat is used in Kingmaker book one, but that's all that comes to mind. You can use part of the Asylum Flip Mat for the first part of Strange Aeons, but it has to be added to.
I find flip mats work best for random encounters or to replace a similar or generic map. Most maps designed for adventures are very detailed and specific and are usually best served by drawing them on a blank mat.
There are several modules that utilize various flip mats or map packs.
Academy of Secrets uses the Magic Academy Map Pack.
Crypt of the Everflame uses the original dungeon flip mat.
The City of Golden Death uses the Ancient Forest Map Pack.
There are probably several more, but I don't know which ones use which mat.