In theory I believe you can unlock and remove the system immutable bit with:
chflags noschg /Path/To/File
But how can you do this when you've set the bit as root? I have a file that is locked, and even running this command as root will not work as the operation is not permitted.
I tried logging in as Single-User mode to no avail.
I seem to remember that even though you are in as root you are in at level '1'. And to be able to remove the system-immutable flag you need to be logged in at level '0'. Does this have something to do with this issue?