Learn Farsi: این یعنی چه؟

In English, we move question words like "what" to the very beginning of the sentence. In Farsi, question words usually stay in the exact same spot where the answer would go. Since the answer would be "This means [X]", the question is structured literally as "This means what?" (In ya'ni che?).

Where is the helping verb "does" in this Farsi sentence?

Farsi doesn't use helping verbs like "do" or "does" to ask questions. You simply use the subject and the main verb. Here, you just say "this" (in), "means" (ya'ni), and "what" (che).

Is ya'ni (یعنی) treated as a normal verb here?

Yes, in this sentence it translates directly to "means." However, you will also hear ya'ni used constantly in casual speech as a filler word, very similar to how English speakers say "I mean..." or "you know..." in the middle of a sentence.

Will I hear people pronounce che (چه) exactly like this in real life?

In formal Farsi and reading, yes. But in casual, everyday speech, Iranians almost always change che (چه) to chi (چی). Because of this, you will most often hear this phrase spoken as In ya'ni chi?.