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You can do this if you make your stylesheets modular. In every place where user is expected to insert something place call for named template (xsl:call-template). This template will be empty by default.
Then deploy your stylesheet as two files -- main stylesheet and driver that will just import main stylesheet. Users will use driver stylesheet and once they want to modify something they can redefine appropriate named template in driver file.
Such way in a future you will just distribute main stylesheet after changes because all customizations will be stored in the driver file.
If you want more straightforward solution you can try to fiddle with tools like XmlDiff to propagate changes from user back to metadata that were used to create stylesheet dynamically.
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