In former times (over 10 years ago) everything was saved in the Administrators server or web context. If you wipe it out, you loose the settings. But that has changed because of exactly that issue you had and for portablity. The vast number of these settings have been migrated to be set within your Application.cfc. You should add all these configurations like datasources, mailservers, mappings, charsets, session configs and everything else to your Application.cfc. The Lucee Administrator also offers a wonderful export tool to copy all these settings to your Application.cfc.
If you can’t use it, you should use tools for backing up these settings, such as CommandBox with cfconfig.
Also, make sure to move and create your scheduler tasks tag based with cfschedule.