FileVault off or on when repairing permissions and updating software?

Does anyone know if FileVault can be left on when repairing permissions and installing apple software updates. I have been turning it off before doing so, but not sure if that's needed. I've been doing that just to be on the safe side.
Using an iMac DVD, with an external firewire HD with OS X 10.3.9 on one of the partitions.
Thanks for any info
iMac DVD +   Mac OS 9.1.x   G3

FileVault only affects your home folder. Permissions repair repairs only permissions on installed OS packages, which are in system folders. Apple software updates make changes to system folders. Since the system folders aren't affected by FileVault, leaving FV on shouldn't affect these operations.

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