I don't use the second one.

“你是什么时候回来的？” -----“是...sth....的”is a structure to express the past situation and “sth.”is the emphasized part, so this sentence indicated that you have already come back and “什么时候”is the emphsized part. “你什么时候回来？”（no “了”in the end of the sentence.）-----It's a normal question and indicate that You still don't come back. Hope it helps~

The former is correct，the latter may be a little weird，and the meaning is “When will you come home” as the “了” is separated from the latter statement.

Thank you, Warren, Cici and Lampard. The one with an Armenian name: I don't know how that video is relevant to my questions or learning Chinese?

你是什么时候回来的？ What time was it when you came back? 你什么时候回来了？ When did you come back?