My recommendation is if you're not sure, disconnect the host from SAN before start the upgrade.
Here are some steps to prepare for the upgrade from the following KB article: Best practices to install or upgrade to VMware ESXi 6.0 (2109712) | VMware KB
To prepare your system for the upgrade:
- Check if the version of ESXi or ESX you are currently running is supported for migration or upgrade. For more information, see the Supported Upgrades to ESXi 6.0 section in the vSphere Upgrade Guide.
- Check the VMware Compatibility Guide to ensure that your host hardware is tested and certified as compatible with the new version of ESXi. Check for system compatibility, I/O compatibility (network and HBA cards), and storage compatibility.
Note: It is not recommended to upgrade a host with hardware that is not certified for use with ESXi 6.0. If your host model is not on the VMware Compatibility guide, VMware recommend you contact your hardware vendor, and check if they plan to support your hardware devices on ESXi 6.0.- Ensure that sufficient disk space is available on the host for the upgrade or migration. VMware recommends a minimum of 50 MB free disk space on the installation disk of the host you are upgrading.
- If you use remote management software to interact with your hosts, ensure that the software is supported and the firmware version is sufficient. For more information, see the Supported Remote Management Server Models and Firmware Versions section in the vSphere Upgrade Guide.
- If a Fiber Channel SAN is connected to the host, detach the fiber connections before continuing with the upgrade or migration. Do not disable HBA cards in the BIOS.
- Ensure you have sufficient access to VMware product licenses to assign a vSphere 6.0 license to the hosts post upgrade. After the upgrade, you can use evaluation mode for 60 days. For more information, see the Applying Licenses After Upgrading to ESXi 6.0 section in the vSphere Upgrade Guide.
- Back up the host before performing an upgrade. If the upgrade fails, you can restore the host.
The KB talks about the Fiber Channel SAN, but the same apply to iSCSI SAN.