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But when I look for pin configuration for HSMC on User Manual of DE2-115, It doesn't match with previous one I mentioned. So, I am a afraid of using it like may be it damage the board.
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What are the differences that concern you?
So long as the pin numbers correspond to pins on the connector, the names do not matter.
Look at the schematic of the DE115 and create a table of the net names used in the schematic and the corresponding FPGA pin number. Then add a column for the two different pinouts you have. That will help confirm that the names used in the VHDL examples map to pins that are GPIO.
Successful synthesis with Quartus will also tell you that the pin assignments are valid. However, it will not tell you that the pins you have used actually route to the GPIO header - since that is board specific.
Cheers,
Dave