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

Exactly the same problem here. External Seagate Expansion drive (used as TimeMachine backup drive) connected directly to my iMac. No problems until El Cap, and the 10.11.1 update hasn't fixed it.

SMC reset didn't fix anything and the issue comes back as soon as I attach the drive again to my cinema display.

After a few days with 'Power Nap' switched off, nothing has disconnected from the back of my iMac - USB 2 bus powered, USB3 bus powered and mains, Firewire via Thunderbolt mains and eSata via USB 3 mains.

That seems to have fixed it for me.

I'll try turning off Power Nap again and see if that doesn't fix my problem as I thought it had once before. My external USB 3 drives are also buss powered.

Update: I reset SMC again after 10.11.1:

Resetting the System Management Controller (SMC) on your Mac - Apple Support

And turned off Enable Power Nap in Energy Saver. Seemed to work yesterday.

Not sure which if either or both did the trick. Turning off Enable Power Nap is a work-around from an earlier post, thank you.

I don't have Power Nap (iMac mid 2011) but I'll try unchecking 'put hard disks to sleep when possible' in Energy Saver and will see what happens.

I already had 'put hard disks to sleep when possible' unchecked for a while so I'm afraid that won't fix it. My 2011 macbook pro doesn't support powernap. For me the issue is again fixed by connecting the drives directly to my macbook instead of to my cinema display.

I'm afraid all I have to add is, "Yeah, me too." But I will be following this thread for sure.

Yep, me too. iMac with no problem for three years with LaCie 1TB drives....until I updated to El Capitan. Mine reconnect with no issue but the notifications are a PITA.

The issue hasn't occurred anymore since I attached the drive directly to my MBP, but this doesn't seem to be a fix for others.

Strangely, I was at my father this weekend and he has a mac mini with 10.10.4 and he had the same issue for a while (also a Western Digital Elements connected directly to his mac mini), so it doesn't seem to be limited to El Capitan.

My drives have always been connected directly to the iMac without a hub, so it's not that. And it may not be solely due to El Capitan, but in my case, with my drives and setup it actually is, since I have been using these drives for years on earlier OS's and never had this problem until the day I updated to El Capitan.

+1 for SMC reset. My Retina MBP started doing it after upgrade. I use a PNY Storedge to keep my photos on and it would complain every time it would wake up. Did the SMC reset a couple days ago and so far it's not doing it any longer.

Ditto. And the SMC reset didn't work for me.

SMC didn't work here either. I have noticed that it's not EVERY night that I get the DNEP errors. And one time, I got errors for both drives, and one didn't reconnect automatically. Then the last two days it hasn't happened at all....mystifying. At least for a while it was consistent.

I've simply disconnected the power from the drive and boot it up from time to time to perform TimeMachine backups, if I can remember to do so. Not exactly a foolproof backup strategy.