So I've been thinking my alignment is off on my 4Runner. I bring it to my local Toyota dealer today to get it aligned and they tell me my passenger rotor is seized.
He recommends new calipers, turning the rotors, new pads, and new soft brake lines.

I bought Autozone calipers and they have a lifetime warranty. So I'll just swap them out. But what can I do to prevent this from happening again? Will new better brake lines help?

Seized calipers happen when the piston cannot move freely in the caliber bore. I would make a strong guess that the brake fluid was not kept up very well... brake fluid absorbs water from the air and over time too much moisture builds up in the fluids and contributes to caliper component corrosion. Brake basically cannot contribute to seized calipers. I would do a full flush of brake fluid when you install the new calipers.

Will new brake lines help?

I flushed quite a bit when I did the upgrade. About a year ago...

To piggy back on the brake bleed suggestion, here's a video you could use as a tutorial:

These auto parts stores rebuild parts and then resell them. It's not uncommon that these rebuilt parts die an early death. Just get a replacement from Auto Zone and hope you get a better one this time.

From what I understand, the inner lining of a brake line can become detached or something like that and cause a blockage. The positive pressure when you depress the brake pedal allows fluid to flow to the caliper past the blockage put the negative pressure when you release the pedal is not enough for the fluid to return. So, you end up having caliper pistons that won't retract because the fluid can't move freely out of the caliper.

So, I think it's a good idea to get a new brake line whether it's an OEM one or an aftermarket braided steel line.

That makes sense.

OP, you really have 2 options here...

1. Buy new/rebuilt calipers and rotors, install them, flush brake fluid
2. Rebuild existing calipers yourself, buy new rotors, install, flush brake fluid

Add or subtract buying new brake lines as an option on both of these.... so you have 4 total options.

You've almost certainly warped / ruined your brake rotor so you need to buy new front rotors. The brake line theory is possible... they are pretty cheap and not too hard to install, so it's worth doing. If you are are comfortable doing a brake job on your car then you can rebuild calipers... it's not all that hard, but a bit time consuming and dirty. If you would rather just buy parts and put them on I would personally go for option 2 and replace brake lines.

Edit: come to think of it your pads are probably pretty unevenly worn left to right and unevenly heat cycled... you should probably get new pads as well.

Rebuild caliper/pistons, flush system and use only full synthetic fluid.

I've had the exact same thing happen only inverse- the line was deteriorated and blocked and I thought I had a caliper seized in the "open" position. When I disconnected the caliper to replace it I discovered that the caliper was fine but the line was blocked. That was a pretty pleasing discovery since a caliper is way more expensive than a new line!

Thanks for the info Tim!

My reasoning behind Autozone was based upon price, and a lifetime warranty, and knowing that I can swap them out extremely quickly and easily.
I knew going into it what I was doing. I'll also go ahead and get some stainless braided lines. You're the man.

Op, is it possible for you do a autopsy on the sticking caliper before you return it as core?
It would be nice for you if you could see where it froze, and get back to us.

Let me read up on the warranty terms on them and I'll try if I don't think it will be voided. Any autozone specialists care to chime in?

OK so the brake is applied with the seized caliper correct? If you notice any damages to the brake hose, time to get new.

I think if you open the dust boot or anything to show that you mess with it, you pretty much void the lifetime warranty. Just take it back and get another.

Yeah do not do anything other than remove the caliper and return for your replacement. No reason to take chances.