"If you had not come, you would not have been gone"
I think it's supposed to be "if you had not come (here), you would not have (ultimately) gone (to that place).
As for what it actually says, I suppose if you never came here you wouldn't have been gone, because you were never here to be gone from here in the first place. Or something.
I think the "been gone" is the bit that's tripping you up. That's an error. It's "If you hadn't come, you wouldn't have gone," which is a bit of a weird sentence but with the right surrounding context it's fine.
If I got this sentence in a fortune cookie, I'd be really confused, lol.