Currently, if the region file is edited by hand and at the same time in-game, the in-game version will overwrite the external edit, unless a /region load is done prior to the in-game edit. This requires however the in-game user to know that the file has been changed manually.

There should be a check before any /region action performed in-game to reload the region file before the in-game command is executed, or ideally a regular check for the file date to reload itself automatically. The Whitelist plugin for example, does such a check.

Alternatively, external commands could be enabled through the command line interface to the console directly. This works at least in linux if the server is running inside a screen, but the plugin does not accept console commands as of now.