I had the same problem.
At first, you probably created the JNI folder. I assume Gradle believes that the folder contains the source files even after deleting the folder and recreates the jniLibs folder itself (and adds the sourceSets line, similar to the code below).
Check your build.gradle application and find the line
sourceSets { main { jni.srcDirs = ['src/main/jni', 'src/main/jniLibs/'] } }
in the Android section and delete it, Sync, and then everything should be fine.
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