So as long as an agreement helps the company financially, even if it violates the law and circumvents the ability of the representative to represent its members, any action to remove said illegal agreement is harmful to said members?

When you make an agreement that gives an outside body control of pay and benefits, even after your representative body leaves (especially with the knowledge that your body has been voted out), you can't act surprised when its challenged.

This has nothing to do with harming the legacy F9 pilots and everything to do with preserving the IBT's legal right to represent those pilots for all matters involving pay and work rules.