The usual, and least expensive key operation, is the "add a smart key" function. This does indeed add a new smart key up to the maximum limit of four such keys, but the old smart key(s) remain. Deleting smart key(s) requires that the ECU be reset, and this takes lots of time as the ECU is cleared. Then, each key is added back into the ECU using a process not unlike an "add a smart key" function. Because of the way the security system works, a simple "add a smart key" function requires one "token" from the licensing company, whereas an ECU reset followed by adding keys as if they were new keys requires additional "tokens". An automotive locksmith which has the required special tools, and the special (and licensed) smart key encoder, can do the job. Each action on his part has an associated charge. Do not be surprised if an ECU reset followed by adding two keys (with the "lost" key thereby being removed) costs many times the cost of simply adding one new key (with the "lost" key remaining within the ECU).
You can delete one key without resetting the entire ecu, only a reseed requires reset of everything. Reseed is when you lose all your keys
Hmmm ... I was not offered that option for my "new to me" (AKA, used) 2012 LB with one fob missing, only a simple "add a smart key" option or a complete reseed. The selling non-Toyota dealer could have provided a second fob with the car, as it also owns a Toyota dealer, but that dealer is in an adjacent state, not in mine. So, I got the car in exceptionally good condition, for a screaming good deal, and I paid for the replacement fob myself (making a total of three out of four fobs in the ECU, two of which I have, and one of which is either in the hands of the trading-in customer, or is "lost").