The Nios® II IDE invokes SOPC Builder during certain operations, which can cause SOPC Builder to change the date stamp of the PTF file even though the system is not modified. This behavior can cause problems if you are using a version control system.
To solve the problem, you can change the PTF file properties to read-only to prevent the Nios II IDE from changing the file. However, you will need read write permission for the PTF file if you are using the Nios II C2H Compiler.