diff --git a/t/t1090-sparse-checkout-scope.sh b/t/t1090-sparse-checkout-scope.sh
new file mode 100755
index 0000000000..1f61eb3e88
--- /dev/null
+++ b/t/t1090-sparse-checkout-scope.sh
@@ -0,0 +1,52 @@
+#!/bin/sh
+
+test_description='sparse checkout scope tests'
+
+. ./test-lib.sh
+
+test_expect_success 'setup' '
+	echo "initial" >a &&
+	echo "initial" >b &&
+	echo "initial" >c &&
+	git add a b c &&
+	git commit -m "initial commit"
+'
+
+test_expect_success 'create feature branch' '
+	git checkout -b feature &&
+	echo "modified" >b &&
+	echo "modified" >c &&
+	git add b c &&
+	git commit -m "modification"
+'
+
+test_expect_success 'perform sparse checkout of master' '
+	git config --local --bool core.sparsecheckout true &&
+	echo "!/*" >.git/info/sparse-checkout &&
+	echo "/a" >>.git/info/sparse-checkout &&
+	echo "/c" >>.git/info/sparse-checkout &&
+	git checkout master &&
+	test_path_is_file a &&
+	test_path_is_missing b &&
+	test_path_is_file c
+'
+
+test_expect_success 'merge feature branch into sparse checkout of master' '
+	git merge feature &&
+	test_path_is_file a &&
+	test_path_is_missing b &&
+	test_path_is_file c &&
+	test "$(cat c)" = "modified"
+'
+
+test_expect_success 'return to full checkout of master' '
+	git checkout feature &&
+	echo "/*" >.git/info/sparse-checkout &&
+	git checkout master &&
+	test_path_is_file a &&
+	test_path_is_file b &&
+	test_path_is_file c &&
+	test "$(cat b)" = "modified"
+'
+
+test_done
diff --git a/unpack-trees.c b/unpack-trees.c
index 2927660d92..d6cf84904f 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -224,6 +224,9 @@ static int check_updates(struct unpack_trees_options *o)
 		struct cache_entry *ce = index->cache[i];
 
 		if (ce->ce_flags & CE_UPDATE) {
+			if (ce->ce_flags & CE_WT_REMOVE)
+				die("BUG: both update and delete flags are set on %s",
+				    ce->name);
 			display_progress(progress, ++cnt);
 			ce->ce_flags &= ~CE_UPDATE;
 			if (o->update && !o->dry_run) {
@@ -293,6 +296,7 @@ static int apply_sparse_checkout(struct index_state *istate,
 		if (!(ce->ce_flags & CE_UPDATE) && verify_uptodate_sparse(ce, o))
 			return -1;
 		ce->ce_flags |= CE_WT_REMOVE;
+		ce->ce_flags &= ~CE_UPDATE;
 	}
 	if (was_skip_worktree && !ce_skip_worktree(ce)) {
 		if (verify_absent_sparse(ce, ERROR_WOULD_LOSE_UNTRACKED_OVERWRITTEN, o))