[Update 15/12/2016] выглядит как начальные ссылка источника уже недействительна, но ответ по-прежнему остается верным.
You can include as many properties as you want, but the total size of all properties cannot exceed 4096 bytes. You can delete a variable by leaving the value blank.
Источник: https://docs.aws.amazon.com/elasticbeanstalk/latest/dg/eb3-setenv.html
The combined size of all environment variables defined for an environment is limited to 4096 bytes. The format of environment variables is KEY1=VALUE1, KEY2=VALUE2, which means that both the value and key of each variable are included in the total. When a platform has one or more predefined environment variables, such as JDBC_CONNECTION_STRING those variables are also included in the total.
Источник: http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/command-options.html