I have environments running 9.4M6, 9.4M4, and 9.4M3. I will hopefully have them all on M6 by the end of the year.
I have been using Management Console 9.4M6 for all of the environments for quite a while now, and some environments have fairly large, complex metadata repositories, and I have not run into any issues...yet.
It is possible to have multiple versions of the BI clients running on the same PC. When invoking the SAS Deployment Wizard, use the options -changesashome -nosasupdate so SAS does NOT go into update mode, instead it will allow you to install a second instance of the BI clients. I found that tidbit here: https://communities.sas.com/t5/Administration-and-Deployment/SAS-9-4M2-and-SAS-9-4M3-installation-on-the-same-client-but-in/td-p/331549.
The solution presented by @SimonDawson would be the preferred way to manage the different versions without potentially introducing any metadata issues.
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