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The DATA on your storage card will remain after a ROM update, but some programs installed there may not continue to work.
Most work fine and require only a copy shortcut to your start menu folder after a ROM upgrade to resume the original launch functionality. They will not appear in your Remove Programs applet like traditionally installed programs.
Other programs have information in the registry, in-ROM system folders, or system databases which would be overwritten during the upgrade rendering them inoperable. I reinstall all programs after a ROM upgrade.
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