I’m looking to change a Honeywell T45 to a Honeywell T6R HW. Y plan system boiler with existing thermostat in the hallway and control box next to the boiler.
Can anyone tell me which wires go where and which ones will become obsolete when I take out the old rotating thermostat from the hallway?
You need to find the other end of the thermostat cable, disconnect all the wires, then join together the two wires that the Live and Switched live were connected to.
There might be a neutral as well which will need disconnecting.
On your picture I see 8 labels and 7 terminals if there is an unused terminal not seen below there is clearly no wire going to it, with Y Plan the normal closed water heating terminal is used, so some thing wrong.
Normally a wiring centre (junction box) is fitted near the mid position motorised valve, into this junction box the wall thermostat is normally wired between the white wire from motorised valve and the central heating run wire from the programmer (time switch).
Much depends on what boiler is fitted, with oil likely no change, with gas depends on make and if opentherm enabled or not.
On @EFLImpudence bottom diagram it does not show Com this is connected to Line internally with some programmers, your old one there are at least one link, but would have expected two.