for i in {1..2} ; do cat *_$i.fastq.gz >>Combined_$i.fastq.gz ; done
This probably won't work well, as concatenated gzip files ; I would imagine you would prefer to use zcat *_$i.fastq.gz >>Combined_$i.fastq
& then gzip; or perhaps better, simply scrap the idea of cat & do this:
for i in {1..2} ; do tar -c *_$i.fastq.gz >Combined_$i.fastq.gz.tar; done
per folder - then to recurse the folders, simply enclose the line above in a further loop, and run this from the top-level folder:
for f in *; do
pushd . ; cd $f
for i in {1..2} ; do tar -c *_$i.fastq.gz >Combined_$i.fastq.gz.tar; done
popd
done
So here, the loop index $f picks every folder; saves your place; cd's to the folder; executes the loop; returns to original directory & loops again.
The pushd / popd are there to ensure an error doesn't have you roaming the filesystem! Not strictly neccesary, but useful to learn.