Hey, yeah, unfortunately we haven't updated the server.example.properties file in a long time 
Probably it makes sense to incorporate this in the build process, so a new example file is always generated 
But a new config file can be generated by deleting the file, then starting a server.
However, what do you mean exactly with "weather effects don't seem to have any effect"? 
Does that mean the temperature has no impact on the player? Basically the temperature is controlled by the permissions (if notemperature under "general" is set to true, temperature won't have any impact on players).
There is also a hidden option for the server.properties to overwrite this permissions: this is only relevant if Permissions_OverrideNoTemperature was excplicitly added to the server.properties.
Ah cool (excuse the pun) found it.
I was looking in server settings but it's in permissions 
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