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If you created your workspace properly, you should be fine. The only thing the workspace does is sourcing /opt/ros/fuerte/setup.bash this happens in ~/yourworkspace/setup.bash. So if ROS is reinstalled at the same place there should be no problem I think.

To uninstall ROS completely (debian packages and their configs) do:

sudo apt-get purge ros-fuerte-*

To reinstall simply follow the instructions from the wiki.

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