Since atlasFX 3.1 a further modification of the server.xml ist necessary.

Open the Apache Tomcat server configuration in a text editor.

Windows: {CATALINA_HOME}\conf\server.xml
Linux: {CATALINA_HOME}/conf/server.xml

Search for the following connector entry:

<Connector protocol="HTTP/1.1" ... maxPostSize="0"/>

Search the declaration of the connector for http. Add the attribute maxPostSize with value 0. This configuration is required until further notice for all new atlasFX versions.