The file system did not change between 3 and 4 so if the LUNs are still presented to the upgraded host they will be accessible by the that host - if you are comeplely finished with those LUNs then remove them from the SAN side and rescan the HBAs -
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As weinstein5 indicates, you don't need to remove them if you still wish to use them. However, you can do so if you have evacuated all VMs and other data (.iso files, etc) that you need.
To properly remove a LUN in vSphere, you should follow the steps in this KB article: http://kb.vmware.com/kb/1015084
Happy virtualizing!
JP
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Not sure if understand this correctly. However I assume you are talking about the entries in the bootloader after the upgrade to ESX 4?
If so you just need to run the cleanup-esx3 command. See http://www.vmware.com/pdf/vsphere4/r40/vsp_40_upgrade_guide.pdf (page 83)
André