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We have a large 100% complete project with many Alignments, Profiles, Surfaces and Pipe Networks data referenced.
While in a dwg for the project, I noticed the expand (+) was absent from the "Surface" listing of the Data Shortcut node listing.
As I began going through the available shortcuts, I learned there were very few data shortcuts listed which were available before.
Browsed to the _Shortcuts Folder, checked the subfolders and a bunch of the XML files have vanished?
Project is on Network & I just verified several other similar projects and everything looks ok.
Alignments subfolder - just a few miscellaneous type, secondary alignments in listing. All primary's gone.
Profiles subfolder - only secondary align. pfl's. All primary's gone.
Surfaces subfolder - completley empty. (should be at least 10-15 surfaces listed).
Pipe Networks subfolder - Most, possibly all of these are present.
We have a lot of projects using the same workflow and I've not seen this occur before.
Several users in our group and many other disciplines have opened some of the files etc. (This isn't unusual for us).
Have to have IT comb through the backups & see if the _Shortcuts folder can be restored to it's pre-damaged state. 
Has anyone else had this happen before or know of any possible causes?
I've never seen this problem before. Our workflow is that the ds are setup inside each project folder, not in a "master" folder as I've see some firms do. This makes it easier for associating multiple drawings to a project. I sincerely hope you find the cause & solution so that we can learn from it.
Lisa,
We have the same workflow as yours here using project specific _Shorcut folders which all have the same relative Data Shortcut "Working" and "Project" folder hierarchy.
I was on this project initially and off it for past 6 months or so, It could be just another "broken beyond repair" story which I've inherited. 
But I have no idea how I could force C3d to remove / accidentally remove, this many shortcuts from the list, short of physically deleting files from the _Shortcuts folder.
Just seems very strange.
Project is in 2014 and was migrated from 2012 (but doubt that has anything to do issue) as we have many other migrated projects without this problem.
These dref's also worked normally for months after the migration.
I've learned since looking into this that the XML files aren't needed per se, once a dwg contains a particular dref, things still update properly.
Just can't add a new dref to a dwg without the XML pointer file.
Still want to restore the list as the project and if (more likely when) something changes we the XML's available.
So, have you even looked into a program called Undelete by Diskkeeper? It runs on the server, has it's own recycle bin setup. The client installs then access the server recycle bins. Several "copies" of the deleted files are kept and able to be restored within minutes. This has saved me countless amount of time and headaches with IT. Our IT dept typically cycles backups on a monthly basis. If a file was deleted 3 months ago it's no longer available. With Undelete, that's not the case necessarily, depending on how you configure it. There's several types of these apps out there, this is the one we use. Saved me several times. The feature I like is that is tells me the username of who deleted the file and when. Then I can go ask "Why?"
I've never seen that. I've had pathing problems when moving to a new release. That's mostly because we have a main folder for the release the project is in. When I work on a 2012 project in 2014 I copy all the files to the 2014 folder and archive the 2012 folder.
The biggest possibility I see is that they were accidentally erased. That's why (against ITs wishes) I keep my own backups of our projects.
You can, of course, open every drawing and recreate the DReferences. But I know you'd rather avoid that.
Allen
Allen Jessup
CAD Manager - Designer
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Well, luckily we have our 126 Data Shortcuts happily back in the _shortcuts folder 
, sure wish we knew how / why though. Thank goodness for backups.
Just learned yesterday, we have another project with this same issue, which was worked on within the same time frame.
Hoping it's just a fluke thing, we'll be keeping any eye on it for a while here.
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