Remove/Overwrite System Files

I vaguely remember reading something about this a long time back, but now Google searches reveal nothing to answer my question.

I have a process that uses a specific telnet.exe application, not the standard windows telnet.exe. Whenever I remove or rename telnet.exe from the \winnt\system32 directory, and place mine there, it is always overwritten the next time I restart the PC. I can probably get around this by changing the environment variables and moving \winnt\system32 behind the directory where my special telnet.exe resides, however this is a band-aid, not a solution.

I?m looking for an explanation as to what is going on and how to resolve the issue. Thank you in advance.