Hi, I have reversed back to 10.11.3 from time machine yesterday, and all problems mentioned above are now gone.
To answer your questions:
- Yes the SSDs are connected with USB.
- No I don't have any "help" or "assistive" software installed as I know in most cases they do more harm than good.
- I have Fusion Drive inside my iMac and SSDs in side external enclosures.
- No I don't have Trim installed.
- I have 50%+ (100G+) free space in the 24x7 SSD
- I have that HDD energy saver option selected but should that be the cause for the SSD not being recognized / mounted on startup?
I spent my whole afternoon and evening yesterday searching and trying to fix the issue, tried all sorts of "solutions" I found online including resetting PRAM, SMC, entering safe mode, etc. but I was without any luck. A little more information about this: after the system reboot not only the SSD was not recognized but also it could not be found in Disk Utility. If I unplug the USB and plug it back again, the disk was back.
Thanks for your help, but since I've already rolled back to 10.11.3, I'll wait to see if newer updates would fix the issue but I really doubt. Since the above problems don't exist in 10.11.3, clearly it's the problem caused by the most recent update (10.11.4).
I've done a bug report to Apple, HOPEFULLY that will help. Rolling back to older system is not always the optimized solution, but I've been doing so more and more often with today's Apple. I'm not the only one complaining about this and that bugs each time Apple , I say it because I have 2 Macs, 4 iOS devices, they all have similar issues.