diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index c62c6df91c5f1ddfbb197aff8b7d12cc7edd215f..2f6624f011d52edcc518358244d2616e4c28e055 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -306,6 +306,10 @@ void CreateBonds::many()
               nadd_bonds,atom->nbonds);
     }
   }
+  // trigger clearing the list of available neighbor list requests
+  // and a full rebuild of them during the next run setup.
+  // otherwise the request from this command may linger around.
+  neighbor->init();
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 489c5bf5d5f4ce5837d42ee64d8fcd04be3103f3..a4219dbecbc271a0c9c136767a970b2a955c6aff 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -407,6 +407,10 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
       break;
     }
   }
+  // trigger clearing the list of available neighbor list requests
+  // and a full rebuild of them during the next run setup.
+  // otherwise the request from this command may linger around.
+  neighbor->init();
 }
 
 /* ----------------------------------------------------------------------