Mac Magically and frighteningly booted to my CLONE?!

I just had a situation where I was working on the desktop of my MacPro and then some folders with drivers that I had downloaded seem to have disappeared.
This was around the time I was trying to install one of these and it wanted to install on the EXTERNAL DRIVE that contains my CLONE of this drive.
I am now finding the disappeared folders on the EXTERNAL DRIVE and have moved these to my desktop.
However, the MacPro was making a slightly mechanical noise yesterday and was running a bit slow with icons slow to show up on the desktop etc.
I'm a new mac user and this has me a bit terrified quite frankly.
I've disconnected the external clone and have the Time Machine backup still hooked up.
Any advice for the newbie?
Thanks.

Hi Cathy,
I was working on the Desktop - like looking at the folders on my desktop - and moving them around and organizing data that was within them so they were better organized. This goes here, that goes there, this folder gets deleted because there is no more data in it etc.
And at some point I returned to the Desktop to print something within one of the folders and they WERE NOT THERE. So I had this "huh?" moment.
And then I started thinking about this issue with Aliases (which I don't understand totally) where if I create some kind of Alias for my MacBookPro on my MacPro and put this in some kind of place such as (I guess) the Finder Sidebar - Mac will "helpfully" "resolve" it to point to something on my MAC PRO. I create an Alias for MBP Documents folder and then I put it somewhere on the Mac Pro and it all of a sudden points to Documents on the Mac Pro instead of Documents on the MacBookPro which is what it was pointed to initially.
Anyway, this is so problematic I now have a "screenshots" folder on my MacPro and a "screenshots_MBP" on my MacBookPro so there is no way they can get mixed up like this. ALSO, it helps for me to see where I am on the network if you follow me.
This thing about Short Names and Long Names I have to be honest I totally don't yet understand but I hope to soon.
ANWYAY, the point is that I just ran a CLONED backup to an External Drive recently so that I have a full clone of my system in addition to my other backups and I started to think about why these folders had been there and then suddenly disappeared.
So I went looking in the Desktop folder on the EXTERNAL CLONE and sure enough they were there. On the clone but not on the MacPro. So I posted this thread.
I mean, I am sure there are other explanations for what happened both in terms of what I was actually doing or in terms of what happened but this is my recollection. Not possible?
Thanks and regards.

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