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This prints the 2nd occurrence:
awk '/Sub-header1/ && ++n==2 {flag=1; c=3} /^$/ {flag=0} flag && !(c && --c) {print}' filename.txt
You also can give the search criteria as additional arguments:...

Below your example; my awk script will print the lines with <this
##########
'Header1'
'Sub-header1'
X Y
xxxx.xx yyyy.yyy <this
xxxx.xx yyyy.yyy <this
.... ...

Change below statement to be > 0 as opposed to >= 0...
while ((getline < sprintf("Xfile%04d", file)) > 0) print;
Because when end-of-file is reached the >= 0 test will always be true creating an ad...

One reason might be that even though it will work in bash and ksh93, it is not POSIX compliant and so for portability it would be best to use $(cat file)

Why use cat at all? Use the shell itself geo=$(<geom.txt).

What works for "key" would also work for "geom.txt"...

key=345298
geo=$(cat geom.txt)
cat<<eoi>inpfile
Some standard lines of the program that is going to execute inpfile ....
$key
$geo ...

Note that this form will use up a file descriptor for every input file processed. Many awk implementations will run out of file descriptors if this script is given more than about 18 files.

If...

Another solution
awk '{$1=$1;print > FILENAME"_2"}' OFS="\t" file*
This creates new file like file001_2 file002_2 etc.

Close. Try:
for i in file???
do awk -v OFS="\t" '$1=$1' "$i" > tmp$$
cp tmp$$ "$i"
done
rm -f tmp$$
Almost any command that reads and writes a file using the command line syntax:...

Actually, it means exactly what it says... Too many open files. The close() isn't working for some reason. Memory usage is a nonissue, since we're not actually storing anything in memory.

I...

awk 'BEGIN{ cnt=1}
/Generated/ {ofile=sprintf("file%04d", cnt++) ; next}
/Generated/ && FNR > 1 {close(ofile)}
{print $0 > ofile) } ' ...