If this is your only copy of the data, make sure you always have a backup before making changes. Separate fastq-files is rather uncommon, MinION produces .fast5 format (hdf5) which is most commonly converted to a single fastq files (e.g. poretools). But okay.

I assuming you use some flavor of Linux. Theoretically, you would do something like cat *.fastq > combined.fastq But since you have so many files, this might run into problems. After expansion of *.fastq by your shell this will be a very long command. So we'll have to split it up a bit.

I would start with something like the following:

ls *.fastq | split -l 100 -additional-suffix .fastq.list #Make lists of fastq files split by 100 files

for f in *.fastq.list
do
cat `cat $f` > $f.combinedpart.fastq
done

followed by:

cat *.combinedpart.fastq > combinedAll.fastq

Note that I don't have that many files as you here to test the approach above. Feel free to let me know if something doesn't work.