You could sand back to reveal the knots and then block them with the knotting solution. From my experiences of trying to use knotting over a primer, it isn't as successful as putting it on the bare knots.
Zinsser B-I-N can be used on top of the primer and will probably be the best for blocking knots now. The only problem is that it dries super quick, so getting a nice even finish can be tricky.
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