diff --git a/deps/libbdsg b/deps/libbdsg
index 6b871a5a2e8..757896a678e 160000
--- a/deps/libbdsg
+++ b/deps/libbdsg
@@ -1 +1 @@
-Subproject commit 6b871a5a2e8367b97f09f81d59d7d192cff0caa1
+Subproject commit 757896a678eb7af7215147ef38cdb9315775dfe0
diff --git a/deps/libhandlegraph b/deps/libhandlegraph
index 8bb58a35014..ccc11459019 160000
--- a/deps/libhandlegraph
+++ b/deps/libhandlegraph
@@ -1 +1 @@
-Subproject commit 8bb58a3501424ca2876287e383cd650a98608c41
+Subproject commit ccc11459019680ae53b65bcc19077d41ecff3075
diff --git a/src/clip.cpp b/src/clip.cpp
index 8b078619fc9..4b0934fde76 100644
--- a/src/clip.cpp
+++ b/src/clip.cpp
@@ -192,7 +192,8 @@ void delete_nodes_and_chop_paths(MutablePathMutableHandleGraph* graph, const uno
     vector<path_handle_t> path_handles;
     graph->for_each_path_handle([&](path_handle_t path_handle) {
             path_handles.push_back(path_handle);
-        });    
+        });
+    vector<path_handle_t> paths_to_destroy;
     for (path_handle_t& path_handle : path_handles) {
 
         string path_name = graph->get_path_name(path_handle);
@@ -257,10 +258,13 @@ void delete_nodes_and_chop_paths(MutablePathMutableHandleGraph* graph, const uno
         }
 
         if (was_chopped) {
-            graph->destroy_path(path_handle);
+            paths_to_destroy.push_back(path_handle);
         }
     }
 
+    // delete the paths
+    graph->destroy_paths(paths_to_destroy);
+
     DeletableHandleGraph* del_graph = dynamic_cast<DeletableHandleGraph*>(graph);
     // delete the edges
     for (edge_t edge : edges_to_delete) {
diff --git a/src/subcommand/paths_main.cpp b/src/subcommand/paths_main.cpp
index 1fc293df752..d6dd1f4adf8 100644
--- a/src/subcommand/paths_main.cpp
+++ b/src/subcommand/paths_main.cpp
@@ -578,21 +578,17 @@ int main_paths(int argc, char** argv) {
                 exit(1);
             }
 
-            vector<string> to_destroy;
+            vector<path_handle_t> to_destroy;
             if (drop_paths) {
                 for_each_selected_path([&](const path_handle_t& path_handle) {
-                    string name = graph->get_path_name(path_handle);
-                    to_destroy.push_back(name);
+                    to_destroy.push_back(path_handle);
                 });
             } else {
                 for_each_unselected_path([&](const path_handle_t& path_handle) {
-                    string name = graph->get_path_name(path_handle);
-                    to_destroy.push_back(name);
+                    to_destroy.push_back(path_handle);
                 });
             }
-            for (string& path_name : to_destroy) {
-                mutable_graph->destroy_path(graph->get_path_handle(path_name));
-            }
+            mutable_graph->destroy_paths(to_destroy);
             
             // output the graph
             serializable_graph->serialize(cout);