A contract can be varied in accordance with its terms
Many contracts, particularly complex ones or ones with long durations, contain provisions allowing them to be modified. Exactly how depends on the wording of the variation clause(s), but you say this contract explicitly prohibits changes so we don’t really need to consider this.
Contracts can always be varied by a new contract
Notwithstanding the provisions of a contract, parties are always free to vary (or end) a contract by making another contract.
That’s because the rights a contract gives you can always be bargained with just like anything else you own.
Employment contracts are special
What I’ve said above are the general common law rules of contract. However, employment contracts are some of the most regulated contracts and every jurisdiction does them differently because each has a unique history of both law and industrial relations.
You don’t tell us where this is happening but, wherever it is, I can guarantee you there will be specifics of local employment law which will make this situation unique.
So, while the following will be the default rules, your outcome will be different.
Does this clause prevent the union from making mid contract changes?
No
Can mid contract changes conflict with the original agreement?
Yes
Did they have a legal duty to share this side agreement with the members once it was signed by both parties?
That’s an internal governance matter for the union. However, if there was such an obligation and the delegates failed to discharge it, that won’t make the contract with a third-party (like the employer) invalid.