try this:

for f in prefix*.fa ; do
  cat $f >> out.fa
done

I am assuming the question is about how you can concatenate all the same prefix file names at once instead of typing a cat command one by one?

Try this extremely dirty python script:

import os,popen2,sys

prefices = dict([(x.split('-')[0],'') for x in popen2.popen3('ls')[0].read().strip().split('\n') if x != sys.argv[0]]).keys()

for prefix in prefices:
    cmd = 'cat ' + prefix + "* > " + prefix + ".fa"
    os.system(cmd)

Put it in the directory with the fasta files and run it. I would maybe test it out first on a smaller set of fastas. The script defines prefix by anything before the '-' character.

The following uses a perl 1-liner to distribute its standard input into files named systematically after the names of the input files.

# let's put the results in a new subdir.
mkdir merged
perl -wspe 'if ($. eq 1){($o=$ARGV); eval(q{$o=~}.${new}); open(STDOUT,q{>>},$o)}; close ARGV if eof' -- -new='s/(ch\d+.fa_\d+_\d+)_.*/merged\/$1.fa/' *.fa

should put your results in files named, in this case

ch14.fa_20452_206652.fa
ch2.fa_16903_17204.fa