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There might be a conflict, if you have before moved the /xoops_lib and /xoops_data outside of the document root, and/or renamed them, because now XOOPS has your changed /xoops_lib and /xoops_data directories, and the /xoops_lib and /xoops_data that you just copied from the update.
If this is the case, just move content from the new /xoops_lib to your old /xoops_lib, and delete both /xoops_lib and /xoops_data from your XOOPS directory.