The TP9000 which is being removed is wired as below:
View attachment 213301
The remote sensor is an integral part of the TP9000 (albeit remotely located) it should be removed along with the TP9000.
The thermostats do not control the boiler. They are wired to motorised valves that look something like this (other makes are available
)
View attachment 213302
There will be one motorised valve for each zone. When a thermostat calls for heat, the valve opens, when the temperature is reached the valve closes. So in your case, the downstairs zone motorised valve will be wired to the TP9000 and the upstairs zone motorised valve to the TP5000.
That is correct. When the motorised valve associated with each zone is closed by the room thermostat, then that switches off all of the radiators on that zone. This is why positioning of the room thermostat is vital. It should be located in one of the last areas to heat up so that the other rooms are already warm (but not overheated as their TRV's will prevent that) before the room thermostat turns off the whole zone. The radiator where the room thermostat is located should not have a TRV fitted, as one will stop the other working properly.
The two zone approach is a building regulations requirement. So I'm guessing that your home is quite new. The building regulations require that the sleeping areas to be on a separate zone to the living areas. This is for energy saving as it allows the bedrooms to be controlled separately from the living areas, in that the bedrooms can be off during the day or at a lower temperature that the rest of the house.
Which zone the radiators are on is determined by their plumbing connections. Not the controls.