After executing a cold boot on a Windows CE device the operating system performs its fresh inicialization. The same happens when the main and backup batteries get completely discharged and you turn the unit on. If applications and settings are not prepared for such situation you probably have to perform a completely new manual device staging - install all applications and setup all the parametres from scratch.
You can prevent this by using super-persistent storage - which is (on Zebra/Symbol WinCE/WM devices) the \Application folder. Utilizing .CPY and .REG files you can restore files and registry entries into their original locations.
You may find more information about a device persistent setup in Integrator Guides of particular mobile devices.
You can also ask us for preparation of a customer-tailored staging package according to your specific needs. Such a staging package fully automates the initial device setup.