"Prohibit" sign when booting into recently installed 10.11

[macstatic]

In the past few weeks I've done a fresh install of OSX 10.11 on my Mac Pro (mid-2010) on one of its two SSDs. I've previously used 10.9.5 (which is still on the other SSD), so I can boot into either OSX version. I've also spent countless hours transferring all my User files/settings over to the new (10.11) profiles, but then something strange happened today....

First, I woke up my Mac from sleep mode (in 10.11) and there was a error message of some kind which I've forgotten (it disappeared after some seconds before I could get my camera ready), but was something about the operating system not ready or something. Not the usual error messages, but the kind in many different languages at once in white letters with a gray background. I assume it's from the firmware level or at a deep, basic OSX level. I believe I was able to log into 10.11 again after a while, but having rebooted I'm just presented with the "prohibit" sign after a while of booting.
I've tried the following to no avail:

• reset PRAM (CMD-ALT-P-R while booting) a couple of times
• safe mode (SHIFT while booting)
• verbose mode (CMD-V while booting)

verbose mode didn't reveal anything (just a bunch of normal stuff loading, then a long pause and finally the prohibitive sign again).
I am however able to boot into recovery mode (CMD-R) or into the 10.9.5 Mavericks startup disk, so that way I've had access to Disk utility which tells me the 10.11 SSD is OK. I've also looked through the various folders on that 10.11 SSD, and it appears to be perfectly readable (no choking on opening folders etc.).

I've looked up the issue and Apple keeps saying you have to reinstall OSX, which I could do but I have some thoughts about that: first, although I've spent time re-installing all my apps in 10.11 I could do that again if necessary, in addition to 10.11, but my main concern is my users. It's a real pain to manually put files and settings back into a new user, but would a new installation (I have a bootable USB installer of 10.11) let me keep the users and just re-install OSX itself?
I also wonder what caused all this in the first place.
Another page I came across suggest replacing the mach_kernel file. Perhaps that files is available on the 10.11 bootable installer, but even if it is (before actually installing on another drive) I've updated beyond 10.11, so would I need to re-install 10.11 on another drive, go through all the updates for El Capitan, then say access the drive from within 10.9.5 (booting into Mavericks that is, so I can see the (broken) 10.11 SSD and newly installed (and fully working) 10.11 drive and copy the file from there? And can I install 10.11 on a USB stick instead of an external hard drive (all my drives are used for backup purposes)?
Anything else I can try? For instance from the command line when having booted from 10.9.5?

 

[Juicy Box]

Anything else I can try?

It might seem simple, and you may have already tried this, but have you tried holding the "alt/option" key during boot up and see if the drive shows up?

 

[macstatic]

Yes, that works fine. The drive shows up, so everything appears fine. Nevertheless the "prohibitive" sign eventually appears when booting into that drive. I can also choose the drive in the "Startup disk" system preference, so apparently the drive is recognized with one that contains OSX.

I can answer one of my own questions above: yes, it's possible to install OSX 10.11 on a USB stick, which I've now done. I've also applied all the Apple updates so it should be the same as on the SSD.

I didn't quite understand the part about replacing Mach_kernel as I can't find the file. Is it invisible? Is that the core of the OS, so it might actually be what I need (considering everything else appears fine on the drive)?

A less risky solution would probably be Apple's advice to re-install OSX, and from what I read here the "Archive and install" option will keep the files, but just re-install OSX. Does that mean I won't lose either the User folders nor the applications residing on that SSD?

 

[macstatic]

Phew! I'm done and it worked.
That is, I ran the 10.11 installer on that same drive (the SSD with the faulty but still bootable and recognizeable 10.11 on it) and it successfully installed a brand new and fully working 10.11 on it while keeping all my home folders along with the apps I had installed!
A message about this while installing would be nice, but in any case I had backed everything up.

 

[sahnert]

Glad yours is working. I had the same problem with a 2011 iMac.

After a fresh install of 10.13 things worked ok for a while, then froze on waking from sleep and rebooted to the same symbol.

In my case, a clean install did not solve the problem. I had to erase the SSD, install the original OS (10.6) from restore disks, then update to to 10.11, and finally update again to 10.13.

No errors since I completed that process.

 

[macstatic]

Yea, I figured it would be better than "hacking methods" of fixing the existing OS.

It's interested what you say about your SSD because I recently read about having TRIM enabled might cause problems with some SSDs, and I wonder if that might have been the cause of my problems as well.
May I ask which SSD model you've got, and if you had TRIM enabled while re-installing OSX? I have a couple of Samsung 830 models (128 GB) in my Mac Pro, and some website pointed out they're not fully TRIM compliant.