Você pode vinculá-los em um diretório diferente e depois em tar
# find all files in directory named directory
find directory -type f | \
while read f;
do
f2='echo "$f"|sed -e 's/\//:/g'' # replace / with :
ln "$f" "directory2/$f2" # create hardlinks in directory2/
done
Isso criará os seguintes links
directory/file1 => directory2/directory:file1
directory/file2 => directory2/directory:file2
directory/folder1/file3 => directory2/directory:folder1:file3
directory/folder1/file4 => directory2/directory:folder1:file4
directory/folder2/file5 => directory2/directory:folder2:file5
directory/folder3/folder4/file6 => directory2/directory:folder3:folder4:file6
directory/folder3/folder4/file7 => directory2/directory:folder3:folder4:file7