Restarting brings black screen

Hello,

(I've asked the following in the "El Capitan" section, but got no answers, so I try it here.)

Suddenly, when I restart (or "Shift" safe boot) my iMac, it goes in a black screen when the progress bar is about 75% ready.

I booted via internet recovery (cmd+alt+R) and checked the Fusion Drive (First Aid), and no issues were found.

I did the cmd+alt+P+R reset.

Then I ran Apple Hardware Test, there were also no issues found.

To backup some new files (my last Time Machine backup is some days old unfortunately),

I used a mini El Capitan installation on a 32GB USB card.

I hesitate with installing fresh El Capitan system over my existing installation (via recovery),

because I'm afraid I could lose my customized settings (and get the default settings back).

Maybe there is a simpler method to fix the boot process?

Many thanks.