whenever you install Custom Properties component all relevant fields, tables, joins, translations are lost, forever.
This "gruesome" behaviour is recommended for all components, so that, upon uninstalling, the component is _completely_ removed.
Upgrade Starting from version 1.98 Custom Properties features a full-package installer that is capable of upgrading previously installed component, DB, modules and plugins at once.
Nevertheless we strongly recommend to perform a complete backup of site and database before attempting any operation. Better safe than sorry, you have been warned.