I agree the rules about car rental contract change can be quite frustrating. Yet there is insufficient information presented by your question to answer you completely in this forum.
For instance, it is unknown whether what you describe will be viewed as an unfair business practice or legitimate rule applied to everyone fairly and transparently.
The first thing I suggest is that you carefully review the agency's terms and conditions posted online or on your reservation contract.
Note that car rental agencies are regulated in New York by various agencies including State Attorney General Eric Schneiderman. His office may be interested in hearing from you if a consumer fraud has been committed. I have provided a link to his office dealing with car rental practices and tips for consumers in New York. It is a starting point. You can also speak to a private consumer lawyer if you feel you wish to go further after speaking with the regulators in Albany.
I hope this insight is helpful to you. Good luck in getting this matter resolved to your complete satisfaction.
This answer is provided for information purposes only. It should not be relied upon as legal advice which can only be offered to clients in an office consultation setting when all the facts and circumstances can be fully considered and reviewed.