How to prevent gradle to remove my Modules as orphan modules in intellij after each import

We have a java project with Gradle multi build project. The project is big and we have many modules. We have our iml files under version control.

The environment is working until we are changing something in gradle files and importing gradle. Then it will remove all of our iml files. Sometimes it puts them directly under Locally Deleted Files but sometimes it is asking us that it will remove the orphan modules, and we can restore them if we want. At the same time it creates new iml files. Our iml files names have just one word as name but Gradle creates iml files with whole path of modules as this projectName.subfolder.module name.

We have saved many runConfiguration in project.ipr which needs correct module name, so they works. I tried once to remove all of our iml files and let gradle to create iml files and I changed our runConfiguration in ipr file to use the iml file names created by gradle. Then next time while importing gradle removed again all files generated by it and add the root directory name at beginning of iml files.
So if iml files name created by it first time was projectname.subdirectory.modulename it created a new iml files with this name rootDirectory.projectname.subdirectory.modulename. And when I changed the module names in the run configuration name to the new name then when importing gradle again it removed the rootDirectory from the name of iml files.

My question is if there is a way to configure gradle so it doesn't create new modules? If not is there a way to give the iml file names to the gradle or force it to specific names which doesn't changes.

We are using latest Intellij 2020.1 andwe have gradle wrapper with gradle-6.0.1. Our gradle settings in intellij looks like this:

I have tested to check the option Generate *iml files and uncheck it. But there is no differences it is working at the same way.
The definition of sourcesets looks like this in main build.gradle for whole project:

subprojects {

    apply plugin: 'java'
    sourceCompatibility = JavaVersion.VERSION_1_8
    targetCompatibility = JavaVersion.VERSION_1_8


    repositories {
        mavenCentral()
    }

    test {
        useJUnitPlatform()
    }

    dependencies {
        testImplementation 'junit:junit:4.12'
        testImplementation 'org.junit.jupiter:junit-jupiter-api:5.4.2'
        testImplementation 'org.junit.platform:junit-platform-runner:1.4.2'
        testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.4.2'
        testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.4.2'

        testImplementation 'org.hamcrest:hamcrest-library:1.3'
    }

    configurations {
        runtimeLibraries
    }



    sourceSets {
        main {
            java {
                srcDirs = ["src"]
            }
            resources {
                srcDirs = ["resources"]
            }
        }
        test {
            java {
                srcDirs = ["test/src"]
            }
            resources {
                srcDirs = ["test/resources"]
            }
        }
    }

 
}