if your talking about the factory restore in the Indigo tool, It wont wipe the operating system or any apps.
What it does is wipe whats in the kodi user folder.
That means all the addons and any settings you have put in kodi or the addons.
Doing an Indigo factory restore puts kodi itself back to its default settings like a new kodi install,
but does NOT touch any files or folders outside of the kodi user folder.
With libre, Indigo's factory restore just puts it back to like when you first installed it.
Since libre is basically just a linux OS with kodi as the "desktop environment" it just seems like it wipes everything because its centered around kodi.
If your talking the factory reset on the device itself (Android OS in the Android settings), YES, that way will set the entire device back to its own OS defaults and apps