Best way to determine if two path reference to same file in Windows?

Open both files with CreateFile, call GetFileInformationByHandle for both, and compare dwVolumeSerialNumber, nFileIndexLow, nFileIndexHigh. If all three are equal they both point to the same file:

GetFileInformationByHandle function

BY_HANDLE_FILE_INFORMATION Structure

use the GetFullPathName from kernel32.dll, this will give you the absolute path of the file. Then compare it against the other path that you have using a simple string compare

edit: code

TCHAR buffer1[1000];
TCHAR buffer2[1000];
TCHAR buffer3[1000];
TCHAR buffer4[1000];

GetFullPathName(TEXT("C:\\Temp\\..\\autoexec.bat"),1000,buffer1,NULL);
GetFullPathName(TEXT("C:\\autoexec.bat"),1000,buffer2,NULL);
GetFullPathName(TEXT("\\autoexec.bat"),1000,buffer3,NULL);
GetFullPathName(TEXT("C:/autoexec.bat"),1000,buffer4,NULL);
_tprintf(TEXT("Path1: %s\n"), buffer1);
_tprintf(TEXT("Path2: %s\n"), buffer2);
_tprintf(TEXT("Path3: %s\n"), buffer3);
_tprintf(TEXT("Path4: %s\n"), buffer4);

the code above will print the same path for all three path representations.. you might want to do a case insensitive search after that

See this question: Best way to determine if two path reference to same file in C#

The question is about C#, but the answer is just the Win32 API call GetFileInformationByHandle.