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If I understand correctly you have another admin account that is working fine, then given the situation, I think the easiest fix is to rebuild the broken account preserving its directory structure. It may sound scary but it’s actually quite easy and fast. Before proceeding is always better to make a backup of the sensible files you may have in the broken user's account folder.
First you have to login using the working account then open the system preferences and go to "Users and Groups". From there you have to locate and select the corrupted account and click on the minus button to delete it (maybe you have to unlock changes clicking on the lock icon first).
At this point the system will prompt you with options to "Save the home folder in a disk image", "Don’t change the home folder" and "Delete the home folder". You must select "Don’t change the home folder" to leave the account's home folder as is, in its current location inside Users folder, and then you have to continue by clicking "Delete User".
This way you have deleted the user account but you have preserved all its local data and preferences.
The system may rename the home directory of the deleted user by appending "(Deleted)" to the folder name itself, in this case you have to rename the folder yourself by giving the same name it had previously, e.g if the user’s name is Joe you have to rename "Joe (Deleted)" to "Joe" without any spaces before and after.
Now you have to go back to "Users and Groups" and add a new account by clicking on the plus button, here you have to carefully give the exact same full and short name to the account as the name of the user folder (e.g. Joe) then the system will detect the existing home folder with the same name of the user account and will popup a dialog warning with the option to use that folder for the new account home, you have to click "Use Existing Folder" then, after the setup complete, the account will be restored. Now you should be able to login with the restored account and find all your files and apps working.
Maybe this is not a perfect solution but it not require you to move files from an account to another and for sure is better than modify system files by hand if you don’t have the experience and the know how to do that.

P.S. If you do not have another administrator account there are some other steps (a bit more tricky) involving reboot in Single-User mode to create it before.

Hope this can help.
Worked for me. I have run into this problem on 3 different Macs when upgrading to 10.11.2, 10.11.3 and 10.11.5. All were running El Capitan when updated and all software was up to date. Spent hours and or days the first and second time. Saw your suggestion this third time and it worked like a charm. Had figured out the third party software which was launching at startup and had moved to trash with the functioning user admin account. Then deleted the unresponsive user saving their home folder. Removed "deleted" from the home folder and created a new user with same name as original. Thank you so much for your advice. Beats any ideas Apple gave me.
 
I cannot login into my main account. I do have an extra account with Admin privileges and am very tempted to use enric0's suggestion. I have already tried it in a test account and it worked... but it still scares the hell out of me!

My main problem is that I use Parallels to run Windows and I absolutely must not loose that data.

I have always used the Time Machine. Before taking the plunge, can anyone tell me whether the virtual machine data is saved in the Time Machine and where is it (and whether I can access it and save it from a different account with Admin privileges)? I was told by the Parallels people that it is a .pvm file in Mac HD/Users/Shared/Parallels but I cannot find anything there (and I am sure that I used all the defaults when installing Parallels; in that folder I can only find the folders Backups and Problem Reports...).

Any help will be much appreciated.
 
I found the .pvm file in Documents/Parallels, so it is contained in the Time Machine backup. Went ahead with the procedure and it worked. Everything was kept intact, including the stuff in the virtual machine.

So, thank you very much, enric0, you rock.
 
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Replying to give this thread a bump for anyone else who experiences this issue and to express my thanks to enric0 whose method has resolved this issue for me.

I experienced this issue upon updating to OS X El Capitan 10.11.6 yesterday < https://discussions.apple.com/thread/7623987 >. Using enric0's method I was able to resolve this overnight. Thanks again, it's simple genius and works perfectly. Credit has also been given in the other thread that I started in Apple Discussion Support.
 
Thank you very much everybody and thank you for the credits on the other threads. I'm glad to help :)
 
This fix worked for me today in repairing corruption of the main user account on my MacBookPro 6,2 caused by Apple's El Capitan Security Update 2016-001. Thanks so much, enric0! You are a rock star.
 
<snip>Maybe this is not a perfect solution but it not require you to move files from an account to another and for sure is better than modify system files by hand if you don’t have the experience and the know how to do that.
<snip>Hope this can help.

Thanks so much enric0! I know this is an ancient post, but I was having the same problem today with one of my user's computers, and had tried everything, from re-installing the OS, to clearing permissions, repairing the disk, various Terminal commands, fsck, etc. I have been working on this problem since 8am today (it is now 8:44pm), and your solution worked quickly, and easily. It was probably the fastest solution I've tried today, in addition to being the only one that worked. I feel as though I should have figured it out myself, as it is so clear-cut and it just works, but I will take the gift of being guided by you. Many, many thanks.
 
If I understand correctly you have another admin account that is working fine, then given the situation, I think the easiest fix is to rebuild the broken account preserving its directory structure. It may sound scary but it’s actually quite easy and fast. Before proceeding is always better to make a backup of the sensible files you may have in the broken user's account folder.
First you have to login using the working account then open the system preferences and go to "Users and Groups". From there you have to locate and select the corrupted account and click on the minus button to delete it (maybe you have to unlock changes clicking on the lock icon first).
At this point the system will prompt you with options to "Save the home folder in a disk image", "Don’t change the home folder" and "Delete the home folder". You must select "Don’t change the home folder" to leave the account's home folder as is, in its current location inside Users folder, and then you have to continue by clicking "Delete User".
This way you have deleted the user account but you have preserved all its local data and preferences.
The system may rename the home directory of the deleted user by appending "(Deleted)" to the folder name itself, in this case you have to rename the folder yourself by giving the same name it had previously, e.g if the user’s name is Joe you have to rename "Joe (Deleted)" to "Joe" without any spaces before and after.
Now you have to go back to "Users and Groups" and add a new account by clicking on the plus button, here you have to carefully give the exact same full and short name to the account as the name of the user folder (e.g. Joe) then the system will detect the existing home folder with the same name of the user account and will popup a dialog warning with the option to use that folder for the new account home, you have to click "Use Existing Folder" then, after the setup complete, the account will be restored. Now you should be able to login with the restored account and find all your files and apps working.
Maybe this is not a perfect solution but it not require you to move files from an account to another and for sure is better than modify system files by hand if you don’t have the experience and the know how to do that.

P.S. If you do not have another administrator account there are some other steps (a bit more tricky) involving reboot in Single-User mode to create it before.

Hope this can help.


Worked like a charm -- This saved me such a huge headache! Thank you!
 
I'm wondering if my problem might be fixed following some of this ... I have a USER account that cannot access App Store or use iCloud. If I switch to USER2 or USER3, and I have created them as admins and as standards, then back admin, I have no problem with iCloud or App Store. Can sign in, download, check purchases, etc. And I have used the iPad to verify the MacMini (where all this is happening). But if I try to use USER1 and go to App Store or enter my iCloud information, I get "there is an error connecting to the server." Any suggestions? I've spent about 7 hrs over two days so far. It's not that big deal, I guess, except maybe syncing calendars and mail and getting apps, but the apps are available via the other sources. Just would like it fixed.

I deleted Library/cache files specific to the com.apple/appstore (may not be the actual file name) and I also even created a new APPLE ID. That also works on USER2 and USER3, but not USER1. So, I deleted the info and have gone back to everything now set up as it was/were? :) was. !
 
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