Bukkit

When ever you destroy a portal the info for it in the portals file won't be removed, this can cause problems if you have the chunk load radius enabled as the chunk that had the portal will still remain loaded afterwards. The only way to fix it really is to manually edit the removed gates out of the portals file, or wiping the portals file, but there's no way to reload  the portals config without doing a potential server crashing /reload or restarting the server.

You're almost right. The fact the portal is still in the portals list has nothing to do with whether or not the chunks remain force loaded. When the portal restarts, it checks that a portal actually is present at the given locations, and only force-loads chunks if a portal is still there. So destroying a portal and restarting the server will work. However, you are correct that you *must* restart the server to do this safely. I'll make a note to add a portal refresh command to do this safely at runtime.

https://github.com/akrieger/Nethrar/blob/master/src/org/akrieger/Nethrar/PortalUtil.java#L482 is the only place where chunks are added to the force load list, and that function is only called when creating a new portal after verifying its physical presence (either when entering one or at startup).