APG,
I don't know about Win CE, but in Win 7 Embedded there is a Beckhoff utility (Embedded Write Filter) which lets you lock the SSD (hard drive). Programs think they are writing to hard drive, but actually just temp RAM space. That could be what happened.
The purpose is so the configuration can be locked and come up again when the night-shift Operator's reboot 6 months later to repair the system. It is actually a Microsoft utility you can set w/ one command line entry. Beckhoff simply gives a graphical interface. Downside is that it is about the only user program that ships on a CX. Thus, User's open it, click a few buttons, then close it, not knowing what they wrought (how would I know?).