Q: "Disk Not Ejected Properly" error after EL Capitan goes to sleep and wakes up again.

The problem happens not only when the mac is asleep. It also happens during data transfer.

Wow! That sounds bad. Thankfully, I haven't experienced that. Did you have this problem prior to upgrading to Mac OS X 10.11.4?

Good question. I've been on 10.11.4 for a long time, but the problem started recently. The keep drive awake app did not work for me either.

Our Disksomnia app was created to keep disks awake while the Mac is running (very useful for anyone dealing with media on external drives to avoid the waiting for spin up). Disksomnia won't fix any effect on disconnects caused by the Mac going to sleep.

Add me to the list of people with the "Did Not Eject Properly" problem.

All Hardware is BRAND NEW out of the box 4 weeks ago:

iMac 27" Retina 5k (Late 2015)

El Capitan 10.11.4

External drives:

1. LaCie 2Big 6T Thunderbolt2 RAID 0

(External Power, Thunderbolt directly into the iMac)

2. GTechnology G-Drive 6T USB 3.0

3. GTechnology G-Drive 4T USB 3.0

(Both on external power, both connected to a USB 3.0 hub, connected to the iMac)

From day one, the LaCie 6T RAID has ejected itself ALMOST every time I wake the iMac up from sleep. Never when it was in use. But when I put the iMac to sleep, and wake it up the next morning, the LaCie 6T RAID is gone from the desktop and I get the error message. If I unplug the Thunderbolt cable from the back of the iMac and plug it back in, the LaCie shows up on the desktop and everything is fine.

The GTechnology G-Drives connected with USB 3.0 have never ejected themselves... Always work perfectly.

I tried getting rid of the thunderbolt cable from the LaCie and connecting it with the optional USB 3.0 cable and continued to receive the error message and ejections.

I called LaCie and spoke to two techs. One suggested it was a drive problem and I was going to initiate a return of the LaCie 2Big but then speaking with a second tech, she suggested trying the drive on a different Mac. All I had was an old MacBook Pro running Snow Leopard... I plugged the LaCie into the MacBook via USB 3 and everything worked perfectly. Repeatedly sleeping and waking the laptop re-mounted the drive every time. So it's not the Drive. It's ElCapitan. The tech mentioned something about "Apple changed how thunderbolt ports work starting with Yosemite... that they were shut off or shut down on sleep and they cut off the external drives." She said that they started getting lots of reports of this happening around that time.

ALSO: I tried the Mountain app to try to ease the hassle of plugging and unplugging cables every time I wake from sleep. When I use Mountain to UNmount the thunderbolt drive before sleep, then sleep the iMac, Mountain is supposed to REmount the Lacie thunderbolt drive on waking... but the drive just disappears. Even Mountain can't find it on waking. At least I'm not getting the error message, but I still need to physically unplug the thunderbolt cable and replug the cable for the drive to be seen and remount... every time I sleep my mac.

I just found this suggestion on MacRumors:

http://forums.macrumors.com/threads/disk-not-ejected-properly-error-after-el-cap itan-goes-to-sleep.1928103/page-2

USB3 via a PCi board in MacPro can be dodgy when the computer sleeps. My experience is the power to the board is cut when the computer sleeps and while the board will power back up when the machine wakes, it does not always wake up the drive, which then "disappears". Here is the solution I found: I connected the drive to a powered USB3 hub that is connected to the USB3 board in the computer. The hub power apparently is enough to allow the computer to sleep and allow the drive to wake when the computer wakes. The native USB 2.0 ports appear to handle sleep differently.

This is an interesting idea. Not sure it will work on a MBP, but I'm trying it now.

Okay, so I can confirm that this doesn't work–at least for me.

Reading how this thread has developed, I should add that the disconnects I experienced happened with a computer that is set to never sleep.  Perhaps that is why Keep Drive Spinning works for me -- I also have the "Put hard disks to sleep when possible" box checked, but my sudden disconnects continue to be resolved.  Still, reading how different users have found very different solutions, temporary solutions, or no solution -- points to an issue that Apple ought to investigate.  Bug reports seem appropriate:  https://developer.apple.com/bug-reporting/

Just a quick note - 10.11.4 here now and I can't even complete my first backup with Time Machine due to the disks ejecting, as described here. I don't even know why the mac (brand new MacBook Pro) is going to sleep as I have totally turned off all power nap, disk sleep etc options =(

I have started to just manually eject the LaCie 6T Thunderbolt drive and shut it off before sleeping the iMac. However, when I wake the iMac up, the LaCie 6T thunderbolt drive comes to life, so it's getting some sort of signal from the thunderbolt cable. It does not re-mount, it just spins up. Turning it off and on again does not re-mount the drive on the Mac. THE ONLY THING that works is unplugging and re-plugging the thunderbolt cable. Then it is remounted and everything seems to be fine.

This is all very frustrating. I have tried following the links posted in this thread to submit a bug on the Apple developer site, but I am not a developer. Is there someplace else I can go to bring this issue up with Apple? 

Login to Apple Bug Reporter

I believe you only need an Apple ID.  Should have given this link before.

[UPDATE]

Okay, it looks my initial tests were wrong. I have now let my MacBook Pro go to sleep on its own on 3 separate occasions and I can confirm that this solution, which I mentioned previously, does now appear to work—at least for me and my USB 3.0 G-Drive. I hope others will find this information helpful as well. Here is the solution:

Here is the solution I found: I connected the drive to a powered USB3 hub that is connected to the USB3 board in the computer. The hub power apparently is enough to allow the computer to sleep and allow the drive to wake when the computer wakes.

FWIW, this is the USB 3.0 Powered Hub that I'm using:

http://www.amazon.com/Satechi-Premium-Aluminum-White-MacBook/dp/B00CIY0KUG?ie=UT F8&psc=1&redirect=true&ref_=oh_aui_detailpage_o00_s00

Kelly, you appear to have found something, here.  I plugged the Xiaobi Dual Hard Drive Dock whose disks had been suddenly dismounting into a powered USB 3.0 hub, and -- with the Keep Drive Spinning app's effects disabled (it kept drives mounted for me before this discovery) --  Voila!  They stay mounted.  Time to modify my bug report. 

FWIW, my USB 3.0 powered hub is from Anker  --  http://tinyurl.com/zfqybxm

Awesome! That's great to hear.

I'm at sleep number 6 now and no problems so far. (knocking wood)

Kelly, (and myaka too).

I think you did find a good workaround.  It "sort of" worked for me, too.  Only I had to revert back to 2.0, based on my macmini capabilities.

My macmini was just before the ports were made 3.0.  I had purchased the USB 3.0 hub similar to yours.  I was still getting this problem.  I checked my system info, and found out that the macmini port is 2.0. So I found my old USB 2.0 port (and it also has it's own power source).  I plugged it into the main usb 2.0 macmini port and it seems to be behaving, for now.

My macmini is not that old, so I'm not upgrading anytime soon; I'll just have to keep using the usb 2.0.  Yeah, 2.0 is slower, but my macmini only can do 2.0, so 3.0 usb hub can't make it faster!