[General Questions and Answers] Planterz:
I hope you didn't call them from the phone that's on your account.;)

I really wouldn't worry about returning a phone that is/was rooted, unless perhaps it was a Samsung with Knox tripped and/or a yellow triangle. It's simply not cost effective for them to check every phone. The reps at the store aren't trained for that sort of thing, and when it goes back to wherever they get refurbished, it's only the hardware that gets tested, and they flash a new factory image. They have to flash a new image, because even after a factory reset, sensitive data can still exist in the memory on the phone (data isn't actually deleted when you delete it, until it gets overwritten, formatted, or you use a special app that does that sort of thing). Certain things can remain the same after doing a factory reset as well. I did a factory reset on a Nexus 4 rooted with Towelroot, and root remained.

Case in point: When I was with Verizon, I rooted my Razr Maxx. I was new to this whole "root" thing (I did it to bypass their hotspot crap). I was having a problem with the Play Store; it wouldn't let me purchase/download ROM Toolbox Pro, regardless of if I did it on my phone or off the website. So I got clever and deleted it (with a warezed Titanium - I'm not proud, I paid for the legit version later) and reinstalled it. And every time I tried, the Play Store would FC instantly.

So I did a factory reset, and WTF? The Play Store was GONE. Some bloatware was back, like the Madden NFL demo and some stupid cartoony golf game, but the Play Store was GONE. Not so clever, I guess. So I bit the bullet and took it to a Verizon store, told them I did a factory reset and Play Store was gone (I left out the other stuff). They googled it for like half an hour before giving up and ordering me a warranty replacement.

At one point, a rep did ask me if I hacked it - I played dumb (how do you hack a phone?). If they were trained or experienced in the sort of things we do, they would have known that the only way this could have happened was if the phone was rooted and I did something. And, if I wasn't such a n00b, I would have known to change Play Store to a system app and it probably would have worked fine (this occurred to me the day after). I got the replacement, and never heard anything about the old phone. I didn't feel too bad about "screwing" them in to giving me a new (refurb) phone, because when I got the replacement, I saw that the screen on the old one was dim, yellow, and sickly compared to the newer one, so apparently there was something actually wrong with it. Months later, the battery on the replacement expanded to the point that it popped the screen loose. The battery expanded on it's replacement too. But that's beside the point.

The point is, when you return a phone, it gets tossed into a pile, and that pile gets sent back to whatever it is they do with them. The sales reps aren't trained for that sort of thing - if you have a problem they don't know off the top of their head, they just google it on the iPads they carry around, and if they come across a site like XDA, they probably ignore it because the lingo and jargon here is gibberish to them (hell, most of it's still gibberish to me, and I've been learning all I can for 2 years). So it gets tossed in to a pile and sent wherever, and wherever it's sent gets hundreds of piles a day, and it's simply not cost effective to check every device. The parts get refurbed, the factory images get flashed (to eliminate any residual sensitive data and ensure the version is up to date), and that's that.

So I really, really, wouldn't worry about it. Unless it's a Samsung and you tripped Knox, have a yellow triangle, or it reads as "custom" or whatever. If you unlocked the bootloader, relock it. Beyond that, don't worry about it. I'm not saying it's impossible that something might happen and they "find out", but it's extremely unlikely. And unlikely to have repercussions. Remember, they want your money. Above all, they want your money. Are they going to keep getting your money if they piss you off by not honoring a phone exchange plan that you're already paying more for? Are they going to keep getting your money if you're dissatisfied and choose to switch providers? Unlikely. A new phone to them is a couple hundred bucks. One more year of service is a grand. Don't worry about it.