Whenever you transfer a 'file1.txt' to the machine you should transfer another 'file1.sent' of size 1 byte right after 'file1.txt' has been transferred. You can then have a shell script which checks for these markers and if they show up then you can concatenate the files (if that's what you want).

if [[ -e file1.sent && -e file2.sent ]] then
   cat file1.txt file2.txt > files.txt
fi
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