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Have you reported the loss of your passport to the German police?
They will enter the loss of the passport into the Schengen Information System.
I could find no information about how border guards would deal with the missing entry stamp.
In case this is not clear, the problem is not about the visa (the border guards can see that one was issued in the Visa Information System).
Some form of confirmation when you arrived is what they will be asking about.
Show them the police report of loss of the passport and anything that shows when you arrived (ticket, bill etc.). They only want to know if you overstayed.
Die Passbehörde unterrichtet unverzüglich die örtlich zuständige Polizeidienststelle über jeden Verlust des Passes oder Passersatzes, damit eine Speicherung im INPOL-Fahndungssystem und im Schengener Informationssystem (SIS) vorgenommen werden kann.
The passport authority immediately informs the locally responsible police station of any loss of the passport or passport replacement so that it can be stored in the INPOL search system and in the Schengen Information System (SIS).