In Barbara Tuchman'ss Guns of August she says on the day war was declared that "...[Myron Herrick, the American Ambassador to France] had just recieved a request to take over the German Embassy and hoist the American flag ..." (Emphasis by me)
Why would he be asked to do this? Who asked him to do this, the French or the Americans? Was this a common thing? Was this just some kind of code? I am utterly baffled.
Tuchman's almost certainly referring to the concept of the protecting power. When two nations break diplomatic relations, each typically designates a "protecting power" to take custody of its embassies and protect the welfare of its citizens in the other country. They can also convey diplomatic messages between the parties. For instance, during World War Two, Switzerland was instrumental in both guarding Americans stranded in Germany and in conveying Japanese messages leading up to their surrender. As the protecting power's officials do not formally represent the protected power, they would display their own flag over all buildings for which they're responsible - so, if America was the protecting power for Germany, they would fly the American flag over both their own embassy and the German embassy.
I haven't found anything specifically saying it was the case in World War I, but this is almost a textbook example of what it would look like for Germany to appoint the United States as their protecting power in France.