Yes, there is a way to prevent this. You just need to protect those files or folders that you do not want to overwrite. To do this, you just need to update the protect property of the .fip-destination file located inside the ~ / server / folder .
This is the default value:
protect=mysql/.*,tomcat/work/.*,tomcat/logs/.*,protected/.*,tomcat/conf/tomcat-users.xml
An example of an individual value:
protect=mysql/.*,tomcat/work/.*,tomcat/logs/.*,tomcat/lib/.*,tomcat/endorsed/.*,tomcat/bin/.*,tomcat/conf/.*,tomcat/webapps/elbhc.*,tomcat/webapps/ttsvr/WEB-INF/.*,protected/.*
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