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With GNU find(1), xargs(1), and grep(1):

• duplicate the directory structure:

    cd /path/to/dest
    find /path/to/src -type d ! -path /path/to/src -printf '%P\0' | xargs -0 mkdir -p
  

• restore permissions:

    rsync -a --existing /path/to/src /path/to/dest/
  

• copying files with the given pattern:

    cd /path/to/src
    grep -rlZ pattern | \
        (cd /path/to/dest; \
        xargs -0 sh -c ' \
            while [ $# -ne 0 ]; do \
                grep pattern "/path/to/src/$1" >"$1"; \
                shift; \
            done' sh)