Seems you’re confusing a number of things.
Two comments upfront:
First, you must describe your installation state more clearly. You didn’t even mention which OH version you’re using.
PaperUI implies 2.X but you also say you’ve been using items files and OH for 4 years (when there was no 2.X), both of which hints to a OH1.X version.
Second, Which ‘tutorial’ recommends to use Simple Mode ? Using it only makes sense for beginners.
To avoid confusion: What I understand by ‘Simple Mode’ (and what I’ll be referring to hereby) is the functionality to auto-create items when a thing is created.
You defnitely shouldn’t use Simple Mode if you maintain items in .items files. You shouldn’t use it at all.
It’ll create items whenever a new thing is created, and a thing is (auto-)created when you include new z-wave devices, i.e. you run discovery and your stick exposes new items to openHAB.
And if there already is an entry in your .items file, Simple Mode creates an item, too, and you’ll have two items in the end which is what you’re seeing.
On PaperUI, habmin etc. see this thread.