Dynamic Mapping getting messed up

I am using JDBC input plugin to connect to MySQL databases and get the data to elastic search . I have two configurations to connect to two different databases from the same server .Both config files have different index, document type and fields . With dynamic mapping the indexes are created with fields from both two config files. what is the reason for such case and how it can be solved ?

When there are multiple configuration files, they are merged by log stash. If you do not use conditionals to control the flow, all input data will therefore by default go to all outputs.

Thank you @Christian_Dahlqvist

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