Travel within Schengen is generally free of passport controls. The point is the "generally" which implies that each country has the right to perform passport controls for specific reasons, such as a big sports event (e.g. Olympic games), or e.g. a meeting of the G20. But you can easily avoid these events.

The other - and for you more risky - situation is that you can run any time into a police check, e.g. on the street when they look for drunken drivers or drivers without a valid driving license. Here, your missing passport stamp might be an issue. I assume that you know Murphy's Law: You will have exactly one random check in your whole life - and that one will happen exactly at that time when your passport has not yet the visa "moved" .