You can run an installation with preserving the VMFS datastore(s), which however will require that you re-configure networking, ... and re-add all your VMs to the inventory after installation.
Loosing the host config's isn't a big deal as long as I wont loose the VM's and the host is in eval mode after the install.
If the interactive installation (as of ESXi 5.x) finds an installation on the disk, it will give you the option to
( ) Upgrade ESXi, preserve VMFS datastore
( ) Install ESXi, preserve VMFS datastore
( ) Install ESXi, overwrite VMFS datastore
Depending on which ESXi version is installed the first option could also be named "Force Upgrade, ...".