This article teaches you where your “Pin to Start” goes in Windows 11. Follow the steps bellow, you will find where your “Pin to Start” goes in Windows 11.
I met the same problem. When I set a recently used app to “Pin to Start”, the app shortcut disappeared from Recommended in Startup, and nothing changes in other place. Where does it go?
After carefully checking, I finally noticed that there is a scroll in Startup menu, just here:
At this time, you can move your mouse to Pinned area, and just roll your mouse wheel, and the Pinned items will scroll, and your pinned app will show in that area.
This is where “Pin to Start” items go.