threshold – noun : a level, point, or value above which something is true or will take place and below which it is not or will not

Source: http://www.merriam-webster.com/dictionary/threshold

“You didn’t know that each time you passed the Threshold you were saying good bye” City Limits by Colson Whitehead

This part of the passage meant that each time he went somewhere not knowing that it’ll close down was each a time that he missed a chance to say good bye. He did not know where the threshold was for how long the store will continue to be open for and therefore misses a chance to say good bye each time he goes to that store.