The breather valves (caps) fit into fittings in the valve covers and are not attached to the manifold, and the engine was freshly rebuilt less than 10,000 miles ago, is there any other explanation?

I will say that I recently had work done on my engine and the shop did not reattach my electric water pump power supply correctly causing the engine to overheat, but I shut the engine down before it got too hot, I think.

This problem occurred before the mysterious disappearing breather valves occurred.