It's called the "chain of command." You, of all people, should know that.
Lincoln had no authority to suspend the writ, and no military officer can be lawfully delegated such authority.
What Lincoln wrote to Scott was, "If at any point on or in the vicinity of the military line which is now used between the city of Philadelphia, via Perryville, Annapolis City, and Annapolis Junction, you find resistance which renders it necessary to suspend the writ of habeas corpus for the public safety, you personally, or through the officer in command at the point where resistance occurs, are authorized to suspend that writ."
If General Scott found resistance which rendered it necessary to suspend the privilege of the writ, General Scott personally, or through the officer in command at the point where resistance occurs, was purportedly authorized to suspend the writ. A conditional authorization to do something is not a directive to do anything. There is no evidence to show that the privilege of the writ was suspended by General Scott or anyone else prior to Taney's opinion being issued.
General Scott did not suspend the writ personally. General Keim ordered the arrest, but he was not the officer in command at Maryland and could not even claim apparent authority to suspend the privilege of the writ. General Cadwalader was unaware of the arrest until after it happened and did not receive any apparent authorization to suspend the privilege of the writ until after Taney's opinion was issued.