It is God’s will that all be saved and come to a knowledge of the truth. He doesn’t want any to perish.
However, I also see in Scripture that He draws us and calls us and commands us to repent, knowing that not all will.
He clearly gives us the final choice whether we say yes, to Him or not.
So it’s His will for all to be saved, but it’s also His will for us to make the response. So is God’s will being thwarted?
You've stated it as I believe it.
Are you talking about 2 Peter 3:9? If so, that passage is talking about how God is being gracious by delaying His return. God takes no delight in punishing the unbeliever, so in His great mercy, He delays His return until all that are to be save will be saved.
If God is omniscient, the He already knows who will call on Him. To deny this denies His omniscience, and thus His Deity.
Furthermore, if it is God’s will that all be saved, and yet not all are saved, then God is not omnipotent.
If it up to us to make the response, then we can unmake the response. Otherwise, we lose the unfettered ability to choose.
So either God chooses and we are secure in our election, or we choose, and have the ability to both follow or walk away.
There's a complication. Was God's will thwarted in the garden?