Pressing the "Synchronize" button, will synchronize the filters with the Joomla CMS, deleting orphan filters and generating new.
For example if you created a new Custom Field, a filter will be generated for that. If a new content language is installed and there are categories for that language, your will see new a new category filter for that language.
The synchronization will not change the setup of your existing remaining filters.
Pressing that button, will delete all your existing filters and generate new filters from your system.
Your existing filters will be deleted.