The revelation on Wednesday that President Trump appointed Michael T. Flynn as his national security adviser even though he knew that Mr. Flynn was on the payroll of a Turkish-owned firm with close connections to the Turkish government was accompanied by alarming reports: Decisions that Mr. Flynn made about the war in Syria during his brief tenure appear to have been influenced by his Turkish paymaster.

The administration’s defenders may point out — correctly — that whether or not Mr. Flynn’s policy recommendations while he was national security adviser were made to please Turkey, they did not, in fact, materially affect policy. But the point is that they could have done so.

The main allegation raised in the news media against Mr. Flynn is that he delayed planning for the seizure of Raqqa, the Islamic State’s self-declared capital in Syria. Under plans handed over by the Obama administration, the attack on Raqqa would have involved arming the most effective of the militias fighting the Islamic State in Syria, a Kurdish force affiliated with the Democratic Union Party.

The Turkish government strongly objected to this, fearing it would strengthen Turkish Kurdish insurgents, who have links to the party, and Mr. Flynn’s lack of action is seen by critics as a favor to Turkey. However, a delay was practically inevitable. Deep disagreement between the United States and Turkey over which militia was going to be the main partner in liberating Raqqa — the Kurdish militia or the mainly Arab Free Syrian Army — was bound to hold up the operation regardless of whether Mr. Flynn was pushing for delay.