Some questions:
- Are the users running the software locally, but the files are located on a networked share on your server?
- Are they remoting into the same server you want to remote into, and execute it there?
- If 2. are they executing the files where they are placed on the server, or are they copying them down to a "private folder"?
If you cannot change the location of the files, and everyone is remoting in, and everyone is executing the files in-place, then you have a problem. As long as even 1 user is running the program, the files will be locked. You can only update the files once everyone is out.
If, on the other hand, the users are able to run their own private copy of the files, then I would set up a system where you have a central folder with the latest version of the files, and when a user starts his program, it checks if the central folder has newer versions than the user is about to execute. If it does, copy the new version down first.
Or, if that will take too long, and the user will get impatient (what, huh, users getting impatient?), then having the program check the versions after startup, and remind the user to exit would work instead. In this case, the program would set a flag that upon next startup would do the copying, only now the user is aware of it happening.
The copying part would easily be handled by either having a separate executable that does the actual copying, and executing that instead, or the program could copy itself temporarily to another location and run that copy with parameters that says "update the original files".