This is a follow up to If a party says something about interpretation of contract, is it binding?
If the parties agree to a material change in a contract, but for whatever reason sign the original document, does the change the agreed to still apply?
For example someone is asked to sign a NDA. The NDA is very broad saying "never talk about anything you learn while in this position". If the person asks "can I talk about things that I learned after they become public knowledge" and they receive the answer"yes" but this all happens in a separate communication (e.g. a chain of emails). Would signing the original agreement invalidate the public knowledge part? What if the contract has some sort of integration/merger clause?
Another example is Bob is offered a job and asked to sign a boilerplate employee contract. The contract states that payable hours are only those done in the workplace. Bob asks his manager if he can be compensate for travel time and the manager says yes. If Bob signs the original boilerplate employee contract, does he wave his right to get paid for travel time?
I ask because I know sometimes administratively it may be difficult to change a contract. For example if it's boiler plate or if it's done online and requires replaces a file on a server etc. Is it sufficient just to have written communication even if it's prior to the signing?
This is different than the linked to question at the top, because that asks about clarifying an interpretation, but here I'm wondering about a more substantial change to a contract.
UPDATE: thanks to all who answered. I cannot pick a single correct one...