DO these phrases have the same meaning? It would help if you put them into context (give examples) to be sure. But basically, the answer is yes. There is a slight difference in meaning in that when you say, "It was a part of" implies a single completed action, whereas, saying "It used to be a part of" denotes a habitual action over time.

i think it might depend on a context. but for me it used to be part of.. means that it is not part of the initial subject anymore. but it was before it was part of ... sounds like something is being described and the last time it was seen. it was part of some the subject like if you were looking for a lost thing and the person is describing it how is was the last time he saw it. I am not sure if I am 100 correct. but that's how it sounds to me.