Macintosh HD in trash

Community,

For some reason opened zip files did not show up after opening in downloads, they could be opened from the download menu in Safari, however I used "locate in finder" and they showed up as in downloads anyway. But they could only be seen doing it in this way, closing finder and reopening it and checking the downloads folder still had no effect.

Now after I imported my music to iTunes I deleted this file so I wouldn't have any duplicates.

As usual I delete the items in my trashcan now and then, now I noticed I got some errors, I decided to right click on one of the music files in trash and click delete now. It started deleting it really slowly I thought, however after a few minutes it deleted about 35.000 files, I thought this can't be right and cancelled it.

At this point I noticed that the whole Macintosh HD file/disk was there TWICE. I have no idea how it moved there, maybe because of some virus or because of the way I deleted the music files. I can already guess that I have some system damage now, since it probably deleted all system files that were not in use.

I did not have to type my password while I did the delete now, maybe I got lucky with this and no necessary system run files were damaged but now I'm left with the question.

What can I do to check if I have no system damage, also which files should I make a back up of before restarting?

Unfortunately a couple days before I stopped time machine from making a regular back up because I wanted to use my extern HDD for different purposes.

I'm not able to copy/paste files which gives me the error "-50", to solve this I'm duplicating my:

- Desktop

- Documents

- Photos

- Music

- Movies

- Programs

And moving them to my HDD after, but this is going to take 10+ hours as it's around 500gb of data.

Is there a chance that I will get a system crash and if so how can I minimize this?