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There have been a major change in the structure of Sage between 5.13 and 6.0 (migration to git layout + new packaging system + ...), so you need to reinstall Sage from scratch. However you do not need to uninstall 5.9 to install 6.4.1 (it depends on how you installed it).

There have been a major change in the structure of Sage between 5.13 and 6.0 (migration to git layout + new packaging system + ...), so you need to reinstall Sage from scratch. However you do not need to uninstall 5.9 to install 6.4.1 (it depends on how 6.4.1, they can both coexist in their respective directory since the packages are isolated within a virtual environment (if you installed it).it by uncompressing a tarball in some directory).