Thermostat C wiring issue
You're right: the wiring colors as installed are &quot;wrong&quot; according to convention. The arrangement in the &quot;after&quot; drawing should satisfy the thermostats and operate the system correctly.
Because the wire colors are confusing it may be a good idea to re-mark them. You could get colored heat shrink tubing and use it to put a colored band on each conductor (or use colored tape). Shrink tubing is available in electrical supply and auto parts stores, among others.