Regarding your question on changing oil filters mid stream of a cleaning application, with Auto-Rx Plus. Normally a filter change during the cleaning application is not needed. And it may sound odd, but not all sludge is created equal or the same. In the case of your Toyota motor, I am assuming it is the 24 valve V-6 motor offered in 2002. And if so the sludge issues has a lot to do with the undersized drains in the valve buckets. This allowed oil to sit too long above the high heat of the head and get baked before it could drain down once the car motor was shut down. As deposits developed the undersized draining capability would get further and further constricted. Really a true snow ball effect.
The top end valve train sludge formed in these motors occurred over a long period of time. The deposits are literally baked very hard. That would be opposed to a quick sludging situation that might occur, from antifreeze coolant leaking into the oiling system, which quickly makes a soft pudding type sludge, that cleans up very quickly with Auto-Rx. This is where a filter change would be more likely part way through a cleaning application. In your case, if it is the typical formations of this particular motor the rate of cleaning is relatively slow. I would suggest running a conventional oil for a heavy sludge application. For one reason the cleaning is a bit faster. There is no need to circulate dirty oil any longer than you need to. Auto-Rx is quite methodically in the cleaning aspect. It uses heat, pressure and oil flow to clean. This is why it always cleans the actual working parts first. The frictional surfaces create heat and pressure and the oiling system directs oil to the frictional points. So the good news is key components in the motor clean first, whereas cosmetic areas with less directed oil flow will clean last.
You may want to pull the PCV valve on the motor for examination. The function of the PCV valve is to vent unburned fuel out of the crankcase and back through the intake system for a reburn if you will. They typically get crusty overtime from the fuel and other volitiles in the oil passing through. But it should not have any liquid oil in it or the tubing attached. If it does than you know the oil is having a very tough time draining back to the oil pan. The oil pump is sending oil up to the valve train faster than it can gravity feed back to the pan. Thus flooding under the valve cover occurs. And oil gets sucked right through the PCV valve. If your motor is doing this, then I can say that you are severe enough to likely need two cleaning applications to get this motor's health back to respectable.
