Nios stops after upgrading Hardware from SRAM to DDR3 RAM

Could you share your design? If your mixing SRAM and DDR3 , you need to make sure the instruction and reset vectors are pointing to the correct location. Sometimes if not it can cause strange stuff to happen. Also if DDR3 isnt set up correctly, such as not having the correct timing and such for the board can cause issues. Try to see if you can write and read to the DDR3 with the old setup. If the DDR3 works fine, then try upgrading again. Hope this helps.