I was trying to merge three projects and it did not happen due to differences in the parameters. I have set the coordinate system for all the three projects in UTM 45 N before the initial processing. The horizontal and vertical accuracy were also set as 0.2 and 0.3 respectively before the initial processing. Please let me know the possible causes.
Hi,
Please make sure the output coordinate system of the sub-projects is exactly the same (both horizontally and vertically):
Let me know if this is the case 
Christina