aws cli lambda `update-function-configuration` deletes existing environment variables

You are misinterpreting the intention of the documentation.

You provide only the parameters you want to change.

--environment is the (singular) "parameter" that you are specifying should be changed -- not the individual variables.

The environment variables are configured en bloc so there is no concept of specifying only certain environment variables that you want to be different.

aws lambda update-function-configuration --function-name my-function-name --environment Variables="{VAR1=variable_value, VAR2=variable_value}" 

Description:Above Command will update the environment variables for the lambda function in aws.