Windows CE stores data in RAM using an Internal Files System called the Object Store. The Object Store stores blobs of data. The blobs of data can be files, like a database or document, or the blob can be your thread’s heap or stack. 
Since the Object Store is in RAM, if power is lost to the device that data will be lost. That includes the files that you so carefully created in RAM.
In the Platform Builder Catalog, you can choose the way the Internal File System works. The options that you have for the Internal File System are ROM-Only File System and RAM and ROM File System. It is important to know that the use of ROM refers to the OS image, which may be in ROM, flash or RAM.
What is the difference?
 
ROM-Only File System
RAM and ROM File System
Heap in RAM
YES
YES
Stack in RAM
YES
YES
Files in RAM
NO
YES
 
So from looking at the table, we see that the heap and stack are in RAM for both ROM-Only and RAM and ROM. But the big difference is that files are not stored in RAM in the ROM-Only File System, which means that when you create a file it will not be lost when power is removed from your device if you supply an file system that will persist the files.
For either system, the Object Store is in RAM.  But for the ROM-Only File System you are required to have a file system, like flash, SD Card or Hard Disk, that files can be stored in if you want to create files at run time.  When you use the ROM-Only File System, your non-removable file system can be mounted as the root folder.
There may be many reasons why you would want to choose one system over another. You will need to consider how much RAM and other disk space you have, what your power requirements are, how your system is supposed to work and possibly many other factors when making the choice. 
The articles listed in Summary of Platform Builder Catalog Posts to be of help.

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