Some commentators understand that the persecution which took place was focused on Hellenistic believers.1 Hellenistic believers were Jewish Christians who spoke Greek and met in their separate synagogues (Acts 6:9), those associated with Stephen.2 If it was indeed focused on Hellenistic believers, then the apostles (as well as Jewish Christians who spoke Hebrew) would have been unaffected. It not only explains their continuing presence in the city but also why a vibrant church continues to exist in Jerusalem also later in Acts.3 Though certainly possible, this understanding does raise questions. For example, why would the persecution be limited to a small subset of the Christian community seeing as the whole Sanhedrin was present to hear Stephen’s testimony and they all reacted with anger? Perhaps it is better to understand that the persecution took place for a short intense period of time, so that the apostles left only to return later.4 Either way, persecution did not bring the apostles' leadership to an end.5
1 And Saul approved of his execution.And there arose on that day a great persecution against the church in Jerusalem, and they were all scattered throughout the regions of Judea and Samaria, except the apostles.