For anyone else searching this problem, I've had this happen a few times and believe I've found the reason.
In my case, I have a deployment package with a "content source location" that is on my applications share.
I also have application deployments with source files in a subfolder of that location.
So - I have a folder Applications\Adobe Flash Player, which is the content source for a deployment package and also contains some other files.
I also have Applications\Adobe Flash Player\17, which is the content source for an application deployment.
I've noticed that repeatedly the 17 subfolder is deleted from Applications\Adobe Flash Player. The GUID-named subfolders containing the software update content are not deleted, nor are the other files in Adobe Flash Player.
The 17 subfolder is deleted by the SYSTEM account. I am still testing as the delete behavior is not yet reproducible, but I suspect my issue is similar to that described below (answer excerpted from link).
"
My problem involved software updates. Software updates were configured by my coworker to download and they pointed the content to
download to the root of the share which ended up deleting all source content. I went under Deployment Packages and selected to display the Package Source Path. This revealed a package was pointing to the root. Made a change to the
package to point it to another folder within the software updates folder we have and that cleared the problem."
http://www.windows-noob.com/forums/index.php?/topic/9077-my-content-is-deleting-itself/
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Proposed as answer by
Kerwin MedinaMicrosoft employee
Saturday, June 06, 2015 1:55 AM