Hi @joaquinsae thank you for opening a support topic with us. Any content created while in the SQLite database will be lost when disabling the plugin.
This data isn’t replicated in both databases so you would need to choose one or the other to use. To avoid this happening in the future, you could copy your content elsewhere before uninstalling the plugin so that it is not lost.
When you activate the SQLite implementation, a new database is created. Your old database remains unaltered, and when you disable the module, your site gets back to using its previous, unaffected MySQL database.
I hope this helps to answer your question.