I got into the same problem. The incremental compilation cleans the target/classes and target/testClasses directories. maven-resources-plugin is run before and so the resources are all gone.
Run into the same issue using version 1.2.21 of the compiler plugin and wasted hours before randomly trying this after determining that if I did a ‘clean’ and then ‘package’ the resources weren’t there, but doing another ‘package’ retained them, and figured it might be something to do with Kotlin not recompiling anything the second time around.
This used to work however as I have jar files that contain these missing resources, but reverting to earlier versions of my POM with earlier plugin versions didn’t seem to fix it. It feels like something else is involved but this was the only consistent factor I could find
Also hit the same problem when upgrading from 1.2.0 to 1.2.21.
Fixed by turning off incremental compiling of Kotlin
<kotlin.version>1.2.21</kotlin.version>
<kotlin.compiler.incremental>false</kotlin.compiler.incremental>