They really didn't offer any in-universe explanation on the show, other than saying Alan was the new storekeeper, and him also making the remark, "when I bought the store, they told me it was an interesting neighborhood."
However, SS.org's site says that Mr. Handford simply sold the store to Alan. Alan Muraoka says in the 40 years book that CTW was looking for a younger storekeeper (as most of those who attended the auditions were mostly older, grandfatherly types), and also decided to look for an Asian-American, so those worked in his favor.
I would say while the transition wasn't exactly perfect, I just hope there wasn't a sour taste in anyone's mouth when David L. Smyrl left - but then again, from what we understand, he enjoyed his stay on the show, so surely when he left it was on good terms.