If you love something, let it die.
He cared. God, did he care for the mad genius. He cared so much that his limp came back when he was gone. He cared so much that he always fixed a second cup of tea, just in case his miracle had happened and Sherlock joined him for a cuppa. He cared so much that he soaked his pillow with salty tears each night, both before and after sleep and the inevitable nightmares that followed. He cared so much that he would sometimes go into Sherlock's room and just sit and be immersed in the memories before they, like Sherlock, faded from him forever. He cared so much that he even talked to the skull as he polished the Stradivarius, taking care to remove all dust and keep it gleaming before carefully placing it back in Sherlock's chair.
He cared about Sherlock Holmes. Which was why he had to stop. He had to let the man go because he was gone, dead, had committed suicide and left him alone in the cold and dark and guilt and pain. He had to let the detective go because, despite all his seemingly miraculous work, Sherlock wasn't Jesus, and he wasn't going to raise himself from the dead.
He stopped using the cane, and the limp eventually went away. He stopped fixing a second cup of tea because it was a waste to let it go cold. He stopped crying at night, took sleeping aids to help with the nightmares. He placed the violin and bow in its case and took it, along with that blasted skull, into Sherlock's room, sliding the case under the bed and putting the skull on the table. He closed the door and didn't enter the room again.
It took two and a half years, but he had done it. John Watson had cared about Sherlock Holmes, which was why he had to let it all die.