Q: Disk not ejected properly

Apple still has no answers after 32 pages of complaints? Pitiful. I have two brand new Macs with El Capitan on my domain and have the same issue. Every morning, I come into the office and check both new Mac Desktops and see this error message, Disk not Ejected Properly. I only have one ext hdd plugged in on both Macs, strictly for Time Machine backups. If I cannot backup my Macs, then what is this new OS really for? We need answers and/or a fix. Both macs are updated with the latest Apple updates, yet still receiving the same error message every morning after waking up both computers. I disabled sleep mode and kept them on overnight. This did not resolve the issue at hand. I come in every morning and still see this same error message. I have 6 other Mac Pro desktops with Yosemite installed and no problems with the same ext hdds plugged in for only Time Machine backups. Please fix this Apple!!!

Its very sad to me that due to this issue happening every day on both my quite expensive macs that I have had to revert to booting up with bootcamp and using Win10 instead.  At first to prove that this was not a hardware issue,  which I have now proved its not,  windows logs show no disconnection of usb devices, and overnight backups are always successful.  My macs do not just do this when sleeping as none of them were set to sleep and it often happened while copying files to hard drives.  Apple's non response on this issue has been really annoying and quite disgusting as its obviously an issue and being forced to go to Windows to make it work is quite pathetic.

One part of this I dont get,  why "pull the system configuration folder to the desktop",  this folder cannot be moved nor deleted as the system will not let you,  so making a copy of it on the desktop seems pointless.

I can't see how this solution will accomplish anything other than confusing my Mac naming.  I have had the "disk not eject properly" problem for several years, and have over that time spent tens if not hundreds of hours with Apple on the phone trying to fix it.  I should note that only reluctantly would support allow my question to be passed along to technical.  At that time, about a year ago, I was told that it was the fault of my external drive or external hub.  I have an external HD (raid) running as TM which has (fingers crossed) worked now for several months without more than a handful of dneps.  Likewise, my image archive HD, a WD MyPassport plugged into the iMac worked fine until several weeks ago.  Then in the last few days it repeatly and sometimes rapidly dneped.  When I hooked it into my external powered hub, it worked fine for almost a day.  Then the same thing started happening.  Apple has never addressed this problem wholesale; hasn't included any simple means of diagnosing the problem (if it is one with the drive or connections - my disk utility said the WD was fine).  If the problem relates to some kind of machine address cache which gets dumped in the process of changing the machine name, then Apple should provide a more direct way of deleting that cache.  While I appreciate you effort, I am not about to spend hours reconstructing files etc., if it doesn't work.  Apple should address this issue directly.  At one time I was told they would be; others have gotten a similar indication, but nothing has come of it.

Given the complaints about El Capitan so far, I am leery to update from Yosemite to it.  If, however, it would accomplish the same effect as your workaround, I am almost more comfortable in doing that than the workaround that some Apple employee came up with.  (PS - did she say if this would have to be done each time there is a dnep?  Have you had any more dneps?  What's your OS X?)

I get them all the time with El Capitan, pretty much every day when I come in to work.  It is pretty bad that Apple has never addressed this problem.  Thankfully it doesn't actually seem to cause any harm, at least so far...

I put a new connecting cable from the Mac to the ward drive. No problems whatsoever since, but it did it 100% of the time before.

As with alisonfromulverston I replaced the USB 3.0 cable on my external RAID and haven't had a single DNEP error since. You should try it.

This problem is widespread and persistent.  I have had it on and off probably as far back as Mountain Lion.  At one point I spent 20-30 hours on the telephone with Apple trying to sort it out.  It happens to thousands -- judging by the many different discussion threads in Apple communities as well as other discussions, such as those of HD users, the number could be tens or hundreds of thousands -- of people using all sorts and iterations of Macs (iMacs and laptops) running on every recent OS for whom the OS(NB!) - not the user - improperly ejects external HDs of many different brands, with many different connections (both directly to the Mac and and through hubs).

Somehow my iMac has recently (before I upgraded to El Capitan) stopped dnep-ing the external HD I use for TM.  (One of the curious excuses I got at one time was that I was using the HD as a RAID set and the OS, although it offers the option of setting up TM to a RAID set, somehow couldn't handle it.)  The remaining problem with dneps is with another external HD I use exclusively as an image backup.  After experimentation, I have come up with a limited fix, but one with virtually no risk.  When the external HD is properly mounted, I manually eject it properly from finder and leave it unconnected for a while.  When I reconnect, the iMac finds the HD and it seems to stay found for as much as several days.

I am extremely reluctant to try the alleged fix offered by Robster50.  1) I think those instructions incomplete: what happens to the file moved to the desktop? how does one avoid side effects like loss of connectivity on WiFi and to other cable-connected devices? 2) I am chary of changing the computer name (when I had problems with a new iMac, changing the computer name seemed to complicate the problem).  3) If this is a valid fix to many of the many thousands of problems out there: why hasn't Apple (a) sent out a general advisory or (b) incorporated the process into a major upgrade, as to El Capitan (or even done much the same thing invisibly).

I have had this issue for so long I cannot remember when or which OS it started in,  however I have been running the Release version of macOS Sierra courtesy of Apple for four weeks now,  and it has not occurred once,   I am hesitant but it seems to be fixed.

I hope you are correct.  Have not been able to corroborate yet online and haven't been offered Sierra.  Figure I will wait until Apple tells me its available.

For the past two days, one of my disks has been going crazy with this message.  I am used to coming back to the computer in the morning and seeing one message, but not I come back and wake up the computer, and I am seeing like 8-10 of these messages at one time, for the same drive!  Is anyone else seeing this behavior recently?

Yes.  But on and off.  May happen when Mac "awakes" at night for updates or things that happen through Safari which is a backbone of the cloud environment for Apple.  Would be nice if Apple told us what they have been doing about dnpe s all these years.