This is a reproducer for the environment described:
for ((i=3000; i<=4000; i+=100)); do
touch test-MR${i}-1.nt
done
cat >resonancia.kumac <<'EOF'
close 0
hist/delete 0
vect/delete *
h/file 1 test-MRXXXX-1.nt
sigma MR=XXXX
EOF
This is a script which will run inside that environment:
content="$(<resonancia.kumac)"
for f in *MR*; do
substring=${f:7:3}
echo "${content//XXXX/$substring}"
done >proof.kumac
...and the output looks like so:
close 0
hist/delete 0
vect/delete *
h/file 1 test-MR300-1.nt
sigma MR=300
There are no quotes anywhere in this output; the problem described is not reproduced.