You can also do:

seqkit replace -p .+ -r "scaffold_{nr}" --nr-width 4 input.fa -o rename.fa

pipe into:

awk -F '_' '/^>/ {printf("%s_%04d\n",$1,$2);next;} {print}'

biostars want some text

If you would like to use sed, you can do sth like this-

cat output.txt
>scaffold_1 
ATCGTCGATACGCGA 
>scaffold_2 
GCGTACGATAC
>scaffolt_3
ACTATCTACTTCA

cat output.txt | sed 's/>*_\([0-9]\)/_000\1/' 
>scaffold_0001
ATCGTCGATACGCGA 
>scaffold_0002 
GCGTACGATAC
>scaffolt_0003
ACTATCTACTTCA