Hi
My 30 million line file has a header

chr    start   end strand  ref_context repeat_masked   s1_smpl_context  s1_c_count  s1_ct_count s1_non_ct_count s1_m%   s1_score    s1_snp   s1_indels   s2_smpl_context s2_c_count  s2_ct_count s2_non_ct_count  s2_m%   s2_score    s2_snp  s2_indels   s3_smpl_context s3_c_count   s3_ct_count s3_non_ct_count s3_m%   s3_score    s3_snp  s3_indels...

sed -Ee '1s/s([1-4])/L\1/g' -e '1s/s([5-8])/W\1/g' -e '1y/5678/1234/' -e '1q' file

If your sed is working as expected, then how about using a for loop:-

for file in *
do
   sed -Ee '1s/s([1-4])/L\1/g' -e '1s/s([5-8])/W\1/g' -e '1y/5678/1234/' -e '1q' $file > tmp;
   mv tmp $file
done

I will assume you want to change the header but keep the rest of the 30 million lines. Since the new header has the same length, the following will open file for both reading and writing:

sed -Ee '1s/s([1-4])/L\1/g' -e '1s/s([5-8])/W\1/g' -e '1y/5678/1234/' -e '1q' 0<file 1<>file