Anything of version 5.0, be it Server or Desktop, will upgrade the repository on application start, at the moment when the application tries to access the repository for the 1st time.
If Desktops and Server access the same repository file on a shared folder
Create a copy of this repository and re-configure Server to use it, so that it can be upgraded independently. After Server and Desktops are upgraded, re-configure Server back to use the shared repo file.
If Desktops use a Server-hosted repository via the Server Link
When Server is upgraded to v5, Desktops v4 will temporarily not be available to use the repository until they are also upgraded to v5.
Running projects created in previous versions requires no action. Neither on Desktops, nor on Server. It just works. Of course, if a project created in a previous version is saved in ver.5 then it won’t open in a previous version.
The main difficulty is migrating repositories.