I left a Powershell 4 script running overnight. It had 9,000+ files created (from copy-item).
I came in this morning and the program had stopped with an error, but the console output told me there should be over 121,000 files in the new location, but there were only 649!!!
This is a Hyper-V generation 2 virtual machine running Windows 2012R2 and the SQL 2012. There is no DELETE\REMOVE anything in my Powershell script, only create-item for a folder if it does not exist and copy-item to move files from numerous places to one folder.
I was not able to find anything about missing files in Google with 2012R2.
I'm running it again and will find out if it happens in 2 days. The VM guest shows 53GB free and is a dynamic disk.
The VM is exported each night for backup.