diff --git a/src/LogicalGraph.ts b/src/LogicalGraph.ts
index 37f1815d0..c25d75455 100644
--- a/src/LogicalGraph.ts
+++ b/src/LogicalGraph.ts
@@ -84,6 +84,16 @@ export class LogicalGraph {
             const srcNode = graph.findNodeByKey(srcKey);
             const destNode = graph.findNodeByKey(destKey);
 
+            // if source and destination node could not be found, skip edge
+            if (srcNode === null){
+                console.warn("Could not find edge (", srcKey, "->", destKey, ") source node by key (", srcKey, "), skipping");
+                continue;
+            }
+            if (destNode === null){
+                console.warn("Could not find edge (", srcKey, "->", destKey, ") destination node by key (", destKey, "), skipping");
+                continue;
+            }
+
             // for OJS format, we actually store links using the node keys of the construct, not the node keys of the embedded applications
             if (srcNode.isEmbedded()){
                 srcKey = srcNode.getEmbedKey();
diff --git a/src/Node.ts b/src/Node.ts
index 16790e586..ec0029cae 100644
--- a/src/Node.ts
+++ b/src/Node.ts
@@ -1175,6 +1175,13 @@ export class Node {
         result.paletteDownloadUrl(this.paletteDownloadUrl());
         result.dataHash(this.dataHash());
         
+        if (this.hasInputApplication()){
+            result.inputApplication(this.inputApplication().clone());
+        }
+        if (this.hasOutputApplication()){
+            result.outputApplication(this.outputApplication().clone());
+        }
+
         return result;
     }