How to empty ("truncate") a file on linux that already exists and is protected in someway?

You have the noclobber option set. The error looks like it's from csh, so you would do:

cat /dev/null >! file

If I'm wrong and you are using bash, you should do:

cat /dev/null >| file

in bash, you can also shorten that to:

>| file

You can also use function truncate

$truncate -s0 yourfile

if permission denied, use sudo

$sudo truncate -s0 yourfile

Help/Manual: man truncate

tested on ubuntu Linux

This will be enough to set the file size to 0:

> error.log