I know this is late but executing mvn idea:idea solves the issue.
The command re-generates the crucial IntelliJ IDEA files: ipr, iml, and iws, and thus re-align them with your pom.xml.
Documentation: https://maven.apache.org/plugins/maven-idea-plugin
The plugin is retired but still (as of 05.06.2021) works like magic 🙂