LF does NOT delete/touch any photos in the Photos App. If you use one of them (source/photos) LF holds a reference to those EXTERNAL files but does not have a private copy of them in its own UserMedia folder in the Files App, where all of LF’s media, projects and presets live. If you delete them in the Photos App the external references in LF go blind.
In case you work with files that are in the LF UserMedia folder in the Files App then they are owned by Luma. Everytime you import an object to LF by using ‘OpenIn...LumaFusion’ in any other app these objects are private to LF. They are copies, so are also still available in the source application where you sent them to LF from. To get rid of these original objects you have to go to the ‘owning’ source app and delete them there.
In case you made a copy from somewhere within the Files app to the LF folder in the Files app you also do have 2 copies and can manage them to your liking.
Using the Export facility in LF to create a Project Archive gives you a list with all the possible destinations for your archive. Give it a try in LumaFusion or read the manual if anything shouldn’t be clear, which I don’t think it’ll be...
Regarding external drives:
If you connect anything to the port of your device or an Apple dongle, it will only be available through a native app for your connected accessory or the Photos App.
Unless LumaFusion does team up with 3rd party storage space providers everything physically connected to your iDevice is sandboxed and not accessible through LF. However, LumaFusion provides SMB server connectivity to talk to external drives via WiFi. Have a look in the Manual or on the LF homepage for supported devices.
And reading the manual does also help a lot and is essential for effectively operating an advanced versatile application like LumaFusion...
There is already a new one out for the latest LF release 1.7 (as of October 2018).