I was having the same issue recently, but it seems to have finally been resolved.
It was due to a firmware update on our SAN, which was a significant update (we have a SSD cached hybrid storage array for our VDI environment), and after the update the LUNs on that SAN started showing up in the vSphere client as "Supported" under Hardware Acceleration in the configuration tab of each host, where before the firmware update the LUNs showed up as "unknown" under Hardware Acceleration. According to the VMware ticket that I opened, after they checked the logs, they determined that my SAN did not support the "Hardware Locking" hardware acceleration feature correctly, and they determined that that feature needed to turned off because the question prompt was coming up after a machine got vMotioned to another host during load balancing during a desktop reboot/refresh operation and the machines files on the datastore were still "locked" to the previous host causing the question.
They showed me how to turn off the VMFS3.HardwareAcceleratedLocking feature in Advanced Settings on each host, which also requires a reboot of the host to take affect. This has prevented any more errors from taking place and the questions from coming up in my case.
Has anything changed in your environment recently that may be the cause of the errors?