I sometimes get this error in the J2EE (or JEE) module settings in the project options when changing modules. The settings will not even show what modules are chosen.
Nothing really helped much, only sometimes out of luck it started to work again when closing and re-opening the project or when restarting eclipse.
To fix it, you must update your Eclipse to at least version 18.104.22.168. Then it will work.
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