Thanks Davidbeach. Vector realignment is a complex subject for me, especially when I have to swap terminals, but I will certainly try.
Meanwhile it seems that I made a mistake in stating the problem. I am describing below more accurately.
We have a 3 phase, 26.4 kV incoming from utility in the substation. There is a Dd0 transformer stepping 26kV down to 480 volt. Another DYn1 transformer 150KVA, steps down 480 volt to 120/208 volt for lighting/heating etc. This 120/208 supply is given to 3 pole Auto Transfer Switch, neutral being common with other incoming supply to ATS. The other low voltage supply of 3 phase 4 wire 120/208 volt, is coming to ATS from utility.
Let us say that ATS's first (Normal) supply, which is internally generated in the substation, is A, B, C and N.
The ATS's second (Emergency) supply is coming from utility, is A', B', and C' and N'. The N and N' go to common neutral bar of ATS.
I measured voltages to check if the 2 sources in ATS are in sync. They are not. The voltage measured are A-A' = 120 volt, A-B' = 240 volt and A-C' = 120 volt. (Similarly for B and C phases.) So there is a phase difference of 60 degree between the two sources in the ATS. Both sources have correct phasor rotation. Obviously, We cannot do anything to the 120/208 volt coming from utility.
I wonder if our DYn1 transformer can be externally rewired as DYn3, (which gives additional 60 degree shift) and in that case, will it bring both sources in sync in the ATS ? Thanks.