“There is a certain amount of comeuppance, of getting what you deserve, when you behave this way toward your own good corporate citizens,” said Mr. Gudenius, whose home-expansion plan was rejected by the board last year.

The principal planner for the city’s historic preservation section, Lee Webb, denied that the city was arbitrary but did say it was making more of an effort to explain upfront what kinds of property modifications would be allowed.

The controversy has clearly wearied some in Old Town. The president of the Historic Alexandria Foundation, Morgan Delaney, said in an e-mail message that commenting “would serve no useful purpose.”

Beth Temple, the aide to Mayor William Euille, who has called the shop “inappropriate” for Old Town, said he now had nothing more to say about it.

The store’s arrival was a coda to Mr. Zarlenga’s failed negotiations over his expansion plans. He opened the Trophy Room in 2001, then bought the building in 2006, planning to expand.

He hired architects and a lawyer who had been chairman of the Board of Architectural Review.

After working with a board staff member on plans to raise the roof of a small building attached to the back of the property, he thought he had the panel’s support. But in 2007, the board denied his permit request, and the City Council rejected his appeal.