You can modify the application through the .properties files, typically in oware\lib, oware\medserver\lib and in owareapps\<application>\lib, for example: owareapps\redcell\lib. These are text files you can edit with any text editor. The application does not modify local files during the course of normal system operations. When an administrator or user modifies files, like properties or seed files, best practice is to override the properties as in Overriding Properties. Failing that, note which files changed and back up that data. (This application stores all its operational data in its database.)
Particularly if you reinstall your application, installation recreates some properties files in their original form. If you modified those files since the original installation, reinstallation overwrites any changes. Therefore, it is safest to use the application’s override capacity noted above, or to back up these files.