Best practice, and this is what we have always recommended to our customers, is to install Zend Server from scratch, do the necessary configuration/setup/testing and then switch to production.
This recommendation is mostly relevant when moving to newer major Zend Server/PHP versions (hence the 9 of the ZS version). This is even stronger in our case here: the extensive changes in the PHP 7 specifically and the different extensions, had serious potential in transforming the upgrade into a too fragile and non-reliable process.
In the specific case of Zend being the editor of both Zend Server and PHP, I do not see the recommendation of a fresh install as a best practice but rather as a lack of commitment toward your customers and a lack of confidence in your own products.
It's a shame that Zend does not seem to consider its customers needs: being focused on the product rather than on the customers needs for the product is a trap which breaks confidence.
I wish the very bad experience of the lack of migration possibility between Zend Framework major versions would have tought you a lesson but it seems that you still do not listen.
I know that Zend Framework and Zend Server are different products, and if the community can understand the complexity of migrating source code, for a project that is shipped for free, I think it is way different for Zend Server which is a product sold to professionals expecting full service, and who know that migrating a packaged product is 100% possible if you want to.
You feared that the upgrade might be fragile or non-reliable ? I can understand that this is a sensitive subject, but what made you think that it was not your job to make it rock-solid and reliable ?
As a side note, one of the main reason we buy Zend Server is because it allows us to provide a high level of service to our own customers, because ZS manages software lifecycle, and specifically eases application deployement and upgrades, with a process that is automatized and reliable, easy to test, all this without out shutting down the service. Eat your own dog food...
To conclude, implementing ZS9 on our production server will require an important effort, not the one of adapting our source code to PHP7, but the one of backuping, uninstalling, new install, configuration, new tests, etc. All this adding some risk to my business, because your own lack of commitment.
I did try to be honest, I hope I am not being rude: as a customer, I expect Zend to change its approach toward bringing a service, rather than staying on the low level of bringing a technology.