But he already had those. He just wanted to remove the other seeds.

Intentionally propagating patented genes without a license violates the patent. It doesn't matter that he was in possession of the seeds.

Except that he apparently would have been fine if he was just replanting everything and not applying any herbicides, with only some percent of the plants having the patented gene. Even though that would also be intentionally propagating patented genes.

Right. If he had not intentionally tried to concentrate the patented gene, he'd have been ok. He could have used the defense that he didn't cause the contamination, so Monsanto was to blame. But by deliberately trying to get just the altered seeds (or descendants containing the patented gene) he lost the ability to use that defense.

Which I find strange. "Oh go ahead and replicate the patented gene as much as you want, just don't concentrate it."

The difference is that if mere propagation were problematic, then Monsanto directly harmed him by the contamination. He could use the "unclean hands" defense if Monsanto sued. But if he took deliberate action to concentrate the genes, over and above what would normally be done just growing crops, that defense would no longer be available.

Monsanto's statements that it would not sue for just contamination can be viewed as immunizing them against being sued for that contamination.