The git filter-branch man page states:

  NOTE: This command honors .git/info/grafts and .git/refs/replace/. 
        If you have any grafts or replacement refs defined, running 
        this command will make them permanent.

However the command  does not seem to honor tree (or blob) objects
replacements. The bug can be reproduced (with both git 1.7.10 and in the following simple steps:

1. Setup:
        git init
        for i in a b c d; do echo $i >> f; git add f; git commit -m "$i"; done
        git diff HEAD~2..HEAD~1  # the output is non-empty
2. Add replacement for some tree object
        git replace `git log --format=raw | sed -ne 's/^tree //p' | sed -n 2,3p 
| tac`
        git diff HEAD~2..HEAD~1  # the output is now empty
3. Run filter-branch:
        git filter-branch
4. Verify that unfortunatelly it did nothing:
        git replace | xargs git replace -d
        git diff HEAD~2..HEAD~1  # the output is still not empty

The following work-around works for me for tree objects replacements,
but I don't think it is suitable for inclusion in git sources. Most
probably git write-tree should be changed instead to take both the blob
and tree replacements into account.

diff --git a/git-filter-branch.sh b/git-filter-branch.sh
index ac2a005..68064f2 100755
--- a/git-filter-branch.sh
+++ b/git-filter-branch.sh
@@ -276,6 +276,16 @@ test $commits -eq 0 && die "Found nothing to rewrite"
 # Rewrite the commits
+ m="$(git write-tree "$@")"
+ if [ -e "$ORIG_GIT_DIR/refs/replace/$m" ] ; then
+   n="$(cat "$ORIG_GIT_DIR/refs/replace/$m")"
+   echo "Replaced tree $m with $n" >&2
+   m="$n"
+ fi
+ echo "$m"
 while read commit parents; do
@@ -342,8 +352,8 @@ while read commit parents; do
        sed -e '1,/^$/d' <../commit | \
                eval "$filter_msg" > ../message ||
                        die "msg filter failed: $filter_msg"
-       workdir=$workdir @SHELL_PATH@ -c "$filter_commit" "git commit-tree" \
-               $(git write-tree) $parentstr < ../message > ../map/$commit ||
+       workdir=$workdir /bin/sh -c "$filter_commit" "git commit-tree" \
+               $(write_tree_func) $parentstr < ../message > ../map/$commit ||
                        die "could not write rewritten commit"
 done <../revs

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