As seen in MAGNOLIA-7777, some broken server configuration stays in place upon removal of module.
These problems can be handled by another module (e.g. remove old admincentral module config by new admincentral module).
Some modules are removed without replacement though. Those used to be handled by core module version handler which became really big.

Several proposals were raised that would address this: 

• have some uninstaller module  
• a dedicated tool to handle it..?
• ?