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Do I need to back up the whole server or can I just zip the installation directory, I am thinking in case of a roll-back scenario.
It says in the Bamboo upgrade guide 'The Windows installer deletes the previous version of Bamboo.' I am concerned to revert to 5.9.7 as the last know working environment.
I hope that you have found a solution by now and have upgraded successfully.
If not, you should backup the <Bamboo-home> directory and the Database before attempting and upgrade.
The windows installed will remove the old 'install' files and then the upgrade of the files under <Bamboo-home> and the database are performed when the new Bamboo install starts. There is no way to reverse the modifications to these files and database schema.
To upgrade from 5.9.7 you would need to go via 5.14.
To revert back to the previous version you would need to recover your <Bamboo-home> directory and Database then reinstall the 5.9.7.
Any issues seen during the upgrade feel free to raise a support ticket.
Atlassian support- Bamboo