‘optimize mac storage’ is turned ON
In that case I believe your Mac is working as it should.
Optimize Mac storage should be off if you want the files always on your hard drive.
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From what you report, what they say is backwards.
ON means the Mac will “optimise”, e.g. on it’s own based on it’s own secret algorithm copy files up to iCloud and delete them on your Mac. And that is what you see happening.
OFF means the Mac won’t do that and will not copy/delete files.
Being “ON” sometimes raises havoc [technical term] with apps that expect files to be on the Mac and now part of this optimise cycle.
I have my Macs set to OFF and will keep it OFF.
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Actually, it is not backwards… It is the Apple way… 
The full contents of iCloud Drive will be stored on this Mac if you have enough space.
Maybe, they should add an “only” before “if”. 
@FrMichaelFanous: The thing with “if” is that MacOS will constantly decide for you, “if you have enough space”. And those decisions are … interesting sometimes. If you turn “Optimise Mac Storage” off, MacOS will do nothing and respect what you are doing: everything you store on your Mac will stay there, until you offload (right clicking the file/folder and clicking “Remove Download”) or delete it. My two cents: “Optimise Mac Storage” does make sense for those who have a very small SSD but a lot of data in iCloud (more than can be stored on the SSD). I never would turn on “Optimise Mac Storage” if I wasn’t in this situation.
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Is there a way to always keep a local copy of certain files if you have optimize mac storage enabled? As far as I could tell, the answer is no…
I think that the answer is, no, as you indicated.
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