when i install an ESXi Host i have this options:
* Install ESXi, Preserve VMFS Datastore: This will install a fresh copy of ESXi 5.0 and leave your VMFS datastores intact, this will erase all custom configurations, it's a clean slate basically and you will have to re-add your VMs back to your inventory once you have reconfigured your host server.
* Install ESXi, Overwrite VMFS Datastore: This does exactly what it sounds, it will install a clean copy of ESXi 5.0 and overwrite your current datastores - you will LOOSE all information on that datastore.
When i select "Install ESXi, Overwrite VMFS Datastore" will i loose all data on every attached datastore (SAN) or only the data on my local datastore which i selected for my install?
It will overwrite the VMFS datastore which is used for installing esxi.
For reference there is a KB article also present
My recommendation is to disconnect the host from SAN before install/upgrade, this way you avoid data loss if you accidentally select a wrong disk.
See what official documentation says: Upgrade or Migrate Hosts Interactively
Before upgrading, consider disconnecting your network storage. This action decreases the time it takes the installer to search for available disk drives. When you disconnect network storage, any files on the disconnected disks are unavailable at installation. Do not disconnect a LUN that contains an existing ESX or ESXi installation. Do not disconnect a VMFS datastore that contains the Service Console of an existing ESX installation. These actions can affect the outcome of the installation.