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?

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You need to login in with Single-User mode by holding down Command-S

Then

mount -uw /

and finally:

chflags noschg /Path to/File
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