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Root pruning impact on the next crop?

I have a potted bonanza peach tree in it's third summer. The bonanza is a genetic dwarf but is grafted on standard rootstock. I repotted this tree into a larger pot before it broke dormancy this spring. A few months later and it is looking crowded again. The dwarf top is happy, continues to grow, and I don't think it looks too big for the pot. But the standard bottom is not gonna last another year in the same pot. I either need to repot again or root prune. I know I will have to eventually root prune. If I do this doing dormancy, will that impact the tree's ability to flower and set fruit?