The bibliography in the English Me'am Lo'ez haggadah says of Pri Chadash that it "often strongly attacks the opinions of the Shulchan Aruch. Its strongest language was deleted from later editions." Does anyone know where these deleted parts can be found, or what they consisted of?
A related source: there's a teshuva in Ginas Veradim [yoreh deah klal 3, hilchos nedarim, shailah 3] about a person who moved to a new city. In the old city they had placed a cherem on learning the Pri Chadash's sefarim because of his sharp critiques of the Beis Yosef, and in the new city there was no ban and the shoel wanted to know if he could now learn the sefarim.
There's a modern edition of Shu"t Ginas Veradim with notes, and I seem to recall it having info about this topic. It might be worth checking it up. (I saw it years ago but I think it's relevant.)