I am able to modify the Windows CE Registry from the “Windows CE Remote Registry Editor” application, but none of my registry changes persist on bootup. Is there some special incantation to flush the registry to the disk?
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I ran into this problem before. It is because windows CE is in volatile memory and you are essentially reinstalling it on every boot up. There are other partitions on the device that do persist and if you look at the manual for the device you will likely find certain files/directories that are executed on startup. I was working with a MK590 and it would automatically execute reg files in the programs directory (I think it was that directory). So I recommend reading the docs for your device and putting your registry keys/edits in a reg file to be executed on start up.