I don't see a problem. When Severus sent his Patronus to guide Harry to the sword he knew he had a memory that is verifiably recent in which he casts the same Patronus. So whenever he meets Harry and under whichever circumstances he could either cast his Patronus or show Harry that memory for Harry to understand Severus had been helping him all along. One trait of the Patronus is that it can't be faked.