Hi Abul,
I'm running Spis 4.00 Rc2 on a 32 bit Linux system and solved the same problem by putting the new "gmsh-2.4.1-Linux" -folder in the "SPIS_4_00_0_RC2_Linux_32bits/Thirdpart/Gmsh/Linux-I386" -directory where the old gmsh-2.0.8 folder is situated.
Then you have the change the command line in the "config.py" -file situated in the "SPIS_4_00_0_RC2_Linux_32bits/SpisUI/Bin/" -directory.
Around line 151 it says something like: "GL_CMD_GMSH = r"../ThirdPart/Gmsh/Linux-I386/gmsh-2.3.0/gmsh"
Change this to GL_CMD_GMSH = r"../ThirdPart/Gmsh/Linux-I386/gmsh-2.4.1-Linux/bin/gmsh"
i.e. the location of your new gmsh file.
SPIS should now be running with gmsh-2.4.1
Regards Christian