If the core file is "vars.conf", you want to copy that to some other name (like "new-vars.conf"), alter the contents of that copy as needed, and when you are sure it is ready for use, just:

mv new-vars.conf vars.conf
[download]

(as a shell command) or just rename "new-vars.conf", "vars.conf" (as a step in a perl script -- same thing). That way, no one will ever get a partial (or partially edited) version of the file. Assuming the file is read only once per client process, there won't be any inconsistencies from the client's perspective.