I need to change the ownership of the player owned home to an NPC then switch it back again later on.

How do I do this?

Instead of changing ownership of the house, wouldn't a "tenant" faction be easier? The Player could be always in it and the renter added to it and removed from it as applicable. That way the owner (Player) alway retains access, and you aren't locked out of your own house.

You'd need one per house, of course.

Well I need to have the player denied access, like he is breaking in.

It is a mod to rent out the players houses. On renting out, the key for that house is removed and only given back on ending the rental agreement.

I have new NPC's that appear in the homes once they are rented, but I can't give the ownership only to them.

Then you use SetOwnership. At least you don't have any issue remembering who to give it back to at the end of the lease!

You may still need a faction if more than one NPC (e.g husband and wife, master and servant) will occupy the rental property.

Yes but SetOwnership won't work with interior cells. Also I've just tried changing the ownership of the Players house in the CS and even then it still allows me access and all the chests etc still belong to me.

I think maybe something is messing with the Player owned homes ownership settings. But I don't know what.

It's SetCellOwnership, not SetOwnership.