Giritharan - I had a similar problem once when I programmed a huge part on a DEA and then tried to load it onto a B&S. There are probably a number of solutions for this but I will tell you the one that worked for me - and its simple.

When you put the DEA program into the B&S machine simply add a few manual steps to it at the beginning, measuring the first and second axis. When you measure them simply assign the axis that you want it to be, conforming to the original DEA axis convention (for example). The machine doesn't really care if you are measuring in the -Y and calling it the -X. It still uses the comp map and everything will be fine.

It took me a while to get used to it, too, because we are used to aligning "close" to the machine axes, but if you rotate it in the machine's brain by 90 degrees it doesn't do any harm.

Good luck.
Scott