src folder set as instead of src/main/java folder after build

I imported an existing maven project from eclipse and deleted the eclipse related project files from my project.

I have maven project structure as follows

root

- src

 --main

  -----java

   --------com....

After importing and building src folder is marked as Sources folder. I had to go to 'project structure'->Modules select src/main/java and mark it as 'Sources' folder and uncheck src folder from 'Sources'

The changes are effected, but If I change anything in pom.xml and rebuild the project. IDEA again goes to same issue, src folder is marked as 'Sources' and src/main/java is marked as normal folder.

How can I apply my changes permanently?

IntelliJ IDEA 2016.3
Build #IU-163.7743.44, built on November 18, 2016