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Combine them into one line of two things with paste, shuffle them with shuf, separate them out into two files again. I've done it with awk but you could do it many ways.
$ paste -d : file1 file2 |...

To manipulate both files at the same time, try:
awk '{getline l<f}!x[$0]++{print l>fnew;print}' f=file2.txt fnew=file2.txt.new file1.txt > file1.txt.new