Change IntellIj settings via Run/Debug configuration

Hey together :)

I've got a strange issue during my daily working process and hope you can help me in this case. I found a similar topic (https://intellij-support.jetbrains.com/hc/en-us/community/posts/115000389984-Disabling-of-annotation-processing-is-lost-on-maven-reimport) but there is no solution which fits for me. So I try to describe my problem shortly.

When I work on a local or remote branch and switch back to the master the value for the IntelliJ setting 'Enable annotation processing' for my 'Maven default annotation processors profile' sometimes (not every time) changes. Also when I reimport my maven depencies. I have to disable annotation processing so that my tomcat (and other configurations or build processes) can start/run succesfully.

First of all, is there a way to prevent IntelliJ from changing this value? Otherwise I thought about setting this value via my Run/Debug configuration. Is this possible?

You can find the setting via File | Settings | Build, Execution, Deployment | Compiler | Annotation Processors.

Thx and best wishes 
Martin