You have to escape the escape, or enclose the path in quotes:
String[] command1 = new String[] {"mv output/tsk/dir1/metabolic\\ waste.txt", "output/converted/file16.txt"};
String[] command1 = new String[] {"mv \"output/tsk/dir1/metabolic waste.txt\"", "output/converted/file16.txt"};
You have to use \\
because java also uses \
as an escape character, so "\\"
really just contains one \