Hello
I have a group of files

a1.profile a2.profile a3.profile a4.profile b1.profile b2.profile b3.profile b4.profile

s1_context s1_ref s1_sample s1_% etc

for FILE in a1 a2 a3 a4 b1 b2 b3 b4
do
    sed -i.bak "1s/s1/$FILE/g" $FILE.profile > $FILE.profile.header
done

In bash, using -vx options to log what it's doing, we see exactly the output expected:

for FILE in a1 a2 a3 a4 b1 b2 b3 b4; do sed "1s/s1/$FILE/g" file; done
+ for FILE in a1 a2 a3 a4 b1 b2 b3 b4
+ sed 1s/s1/a1/g file
a1_context a1_ref a1_sample a1_% etc
+ for FILE in a1 a2 a3 a4 b1 b2 b3 b4
+ sed 1s/s1/a2/g file
a2_context a2_ref a2_sample a2_% etc

You are using the -i option, which means inplace-update. Therefore the redirection of standard output is obsolete and nothing should be written to the *.header files.

After the loop, the *.profile files hold the contents with the new headers and the *.bak the original contents.