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The Matlab Favorites can be backed up by copying the shortcuts.xml or shortcuts_2.xml from the right folder. The path to the folder, which containing the shortcuts.xml or shortcuts_2.xml, can be obtained by running “prefdir” command from Matlab command line.
Afterward, You can restore your Matlab Favorites on your newly installed Matlab. To do so, you need to copy the backed-up shortcuts.xml or shortcuts_2.xml into your Matlab newly installed folder. In order for Matlab Favorites to get updated, you need to restart your Malab.
The broken link error is unavoidable if you want to restore your Matlab Favorites into a newer version since the paths to the Doc files are different in different versions of Matlab.
you can work around the issue if you want to restore your Favorites to Matlab with compatible (Help) filing structures such as Matlab 2010a, 2010b, 2011a, 2011b, 2012a and 2012b. to work around the issue you need to update the paths in the shortcuts.xml or shortcuts_2.xml accordingly. For example, if you move your Favorites from Matalb 2010a to 2011b, you need to replace all "R2010a" to "R2011b" on the shortcuts.xml or shortcuts_2.xml.
Please note the filing structure for Matlab2013a (or newer versions) are not compatible with the older one; in the other word, the above procedures does not seem very straight forward for restoring your Matlab Favorites from 2012b and older into 2013 (or newer versions).
It would be great if Mathworks considers IMPORT button on Shortcuts Organizer for Matlab 2013a (and newer verstions) similar to browsers.