Multiple book versions inside directories

Greetings friends,

I recently encountered a strange issue with calibre and wasn't sure where to turn, so I thought I'd ask for help here.

I'm trying to organize my library and found that I have multiple versions of some books or documents in the same format, say PDF. Since I'd sometimes like to keep both versions, I added a "Multi" tag in Calibre and manually copied the second version inside the calibre folder. So far, that has worked out well. However, I just found out that a few of the different versions are missing from the folders. So now I'm wondering if this is calibre cleaning itself up. If so, I should probably come up with a different solution.

So I have two questions you might have answers to:
1. Does calibre remove duplicate versions of files from its structure if they're not part of the database?
2. Do you have suggestions how I could handle different file versions better?

Any help would be much appreciated!

Gil

Edit: I'm using 2.85.1 on Linux Mint 18, if that helps at all.