I don't think the retraining rules specifically mention changing faith or religion as retraining, but retraining the cleric levels works just fine.
Personally I'd make altering the faith of a cleric an RP event (or series of events), and then have him become an ex-cleric when he loses faith in his chosen deity as described under the Code of Conduct-section.
If the deity he is changing his focus to is on good standing or is fairly similar to the old deity (for instance, from Iomedae to Abadar or Sarenrae), I'd use the rules for retraining an archetype, requiring five days and a higher level cleric of the appropriate religion.
If the deity is not on good standing or similar to the old deity (say, from Torag to Gozreh), I'd require him to retrain each level of cleric, though I'd give him an added synergy bonus so each level after the first would take three days of retraining instead of five.
At the end of the retraining period he would be a cleric of his newfound deity.
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The retraining rules cover mechanical changes, so they would be used for class feature changes (if the change of deity compels a change between positive and negative channeling for a character of neutral alignment and/or forces a change of domain(s)). There should probably be an Atonement spell cast by a cleric of his new deity to start off the whole process.
To some extend, it would depend on the nature of the religion and the campaign world. Is the world henotheistic*, proclaimed monotheistic, polytheistic with the Gods forming a pantheon of allied Deities?
Switching out of a monotheistic faith would be difficult, as would swapping to a different God in competing henotheisms. On the other hand, switching from one allied God to a different allied God when both are part of the same pantheon should be fairly easy.
For example, a priest of Thor should find it easy to switch over to be a priest of Odin. However, a Christian cleric should have a difficult time making that same switch.
By the way, I referred to proclaimed monotheism, since if your world is a true monotheism, there would be no other God to which the cleric could convert.
* Henotheism refers to a religion which proclaims that its followers are to follow one and only one particular Deity, but other people are free top worship other Gods.
Thank you for the responses. I was asked by my GM to look into this as I had proposed to him allowing me to switch faiths in the game. My current character, a life oracle, is a worshipper of Milani but I would like to switch to worshipping the empyrean lord Arshea. So before I am to do this, I am to see if there are any particular rules out there or rules that might be similar that should apply to my switching of faiths.