Most of the times, if a train changes it's zone of operation, the numbers will be changed, but the order won't be changed. For example, my screen name - Circar express - was numbered 6043/44 when with SR and is now 7643/44 with SCR. But the CCT-MS train was always numbered xx44, and the return train as xx43 irrespective of zone.
This is the case with SER. In the initial years after independence, most of the long distance trains on the Bombay line of SER were maintained by SER, but the trains on the Madras line were typically by SR. In later years, the trains changed maintenance zones, but the order of the numbers remained the same.