Josephus offers us a list of the Jewish high priests extending from the Hasmonians to the destruction of the Temple in 70 CE. Dating them for the most part is not very difficult, if one follows along in his history of the Jewish people, and if one compares his work with the works of others that concern common personalities such as Roman emperors, and the presidents of Syria and governors of Judea etc. There are, however, difficult places in the list that are a bit confusing, where a strict reading leads to contradictions. One of those places in the list occurs when Paul was taken captive by the Romans cir. 56 CE.
Many authorities believe that Ananias, son of Nebedaius was the Jewish high priest from 47CE to 58 CE. However, others claim he could have held this office only until 55 CE. My own understanding is a bit more limiting than this. Josephus doesn’t come out and say so, but it appears that Jonathan, the son of Annas (the same high priest before whom Jesus appeared in John 18:13), was the officiating high priest throughout much of Felix’s authority over Jerusalem. In fact, Felix has him killed for constantly meddling in his affairs, and we must remember that Paul, himself, refers in Acts 22:5 to the current high priest for verification of what he was telling the Jewish crowd. When Paul, then Saul, left for Damascus, Jonathan could have been the high priest at that time, for he replaced Caiaphas about the same time of Paul’s conversion. So, could Jonathan have been the officiating high priest for a second time during Paul’s arrest in Jerusalem and his imprisonment at Caesarea?
Josephus tells us that during the administration of Cumanus, Felix’s predecessor, that an insurrection took place over the killing of one or more Galileans who were traveling through Samaria to celebrate the Feast of Tabernacles. Cumanus overlooked the incident (accused of taking a bribe from the Samaritans), which provoked the Jews into taking measures into their own hands. The result escalated into a localized rebellion against Rome, but the Jerusalem authorities intervened to stop it. Nevertheless, many died—both Jews and Samaritans, and the matter wasn’t entirely settled by Cumanus.
Both the Jews and the Samaritans sent envoys to the president of Syria, Ummidius Quadratus, who was then at Tyre. Long-story-short, this man was not someone to take lightly. Josephus shows that he wasn’t about to let the least matter go unpunished. He sent Cumanus and the Roman tribune under his charge to Caesar to answer charges there for their conduct in the matter. He crucified all the men Cumanus had taken prisoner. He traveled to Lydda and sent for 18 of the Jewish leaders who were accused of the Samaritans of having something to do with the rebellion and beheaded them. Finally he sent for the most prominent Jewish leaders at Jerusalem which included the officiating high priest, Ananias (son of Nebedaius), Annas (the high priest and then governor of the Temple), Jonathan and Ananias (both sons of Annas) and several other high officials together with a like number of Samaritan officials and sent all of them to Rome to answer to Caesar for the charges against them, but Josephus in Antiquities names only Ananias (son of Nebedaius) and Annas the commander of the Temple as going to Jerusalem in chains.
What can be understood from these accounts? For one thing, King Agrippa was the official Rome used for overseeing the Temple affairs and the conduct of the Jewish high priests at Jerusalem. It had been his policy to change those officiating the high priesthood when misconduct was suspected. Moreover, when Ishmael, the high priest, had gone to Rome to petition Nero concerning a matter about building up a certain wall in the Temple, he was detained there, and Agrippa immediately gave the high priesthood to Joseph Cabi, son of Simon.
It seems to me these matters were very light compared with what occurred during the administration of Cumanus where a rebellion against Rome had begun to occur. Josephus shows that the high priesthood was changed whenever political matters were grave, or when complaints were made over the practices high priests endorsed which had adversely affected other groups. Changes in the high priesthood were made in order to gain changes in policy more favorable to the political authority then governing the Jews. It seems inconceivable to me, that Ananias, the son of Nebedaius, would retain his office over this incident. The logical choice would have been Jonathan, son of Annas, for two reasons. First, he was of the family Rome had originally picked to rule the affairs of the Jews when Herod Archelaus was banished. Secondly, he was, apparently, an able administrator, since King Agrippa had also desired to place him in that office as mentioned in footnote two below.
King Agrippa of Acts 26 was undoubtedly celebrating the Passover when Quadratus sent for the leading Jerusalem officials to appear before him at Lydda. What Quadratus had already done had to have reached the ears of every Jew in Judea by the time of the Passover. If Ananias was not already deprived of that office, he most certainly would have been deprived of it in Rome, when Agrippa used his influence with Caesar to free the Jewish group and punish the Samaritans. Therefore, it is my understanding of these matters that Jonathan was made high priest for the second time, just after the Passover of 52 CE, and by his request Felix was made procurator of the Jewish state. These were the officials Paul faced during his arrest at Jerusalem and imprisonment at Caesarea.
 Josephus: Antiquities of the Jews; book 20, chapter 8, paragraph 5.
 Josephus tells us that Jonathan was offered the office for a second time by King Abrippa, but Jonathan declined asking the king to consider his younger brother, Matthias, whom Agrippa named as high priest cir. 43-44 CE (see Josephus: Antiquities of the Jews; book 19, chapter 6, paragraph 4).
 Josephus: Wars of the Jews, book 2, chapter 12, paragraph 6.
 Josephus: Antiquities of the Jews, book 20, chapter 6, paragraph2 – and compare this with Wars of the Jews, book 2, chapter 12, paragraphs 5 & 6.
 Josephus: Antiquities of the Jews, book 20, chapter 9, paragraph 1.
 Josephus: Antiquities of the Jews, book 20, chapter 8, paragraph 11.
 Josephus: Antiquities of the Jews, book 20, chapter 6, paragraph3 and compare chapter 8, paragraph 5.