diff --git a/app/api_topologies.go b/app/api_topologies.go
index 595241b17..c1e1d100d 100644
--- a/app/api_topologies.go
+++ b/app/api_topologies.go
@@ -479,6 +479,7 @@ func (r *Registry) makeTopologyList(rep Reporter) CtxHandlerFunc {
 			respondWith(ctx, w, http.StatusInternalServerError, err)
 			return
 		}
+		report.UnsafeRemovePartMergedNodes(ctx)
 		respondWith(ctx, w, http.StatusOK, r.renderTopologies(ctx, report, req))
 	}
 }
@@ -579,6 +580,7 @@ func (r *Registry) captureRenderer(rep Reporter, f rendererHandler) CtxHandlerFu
 			respondWith(ctx, w, http.StatusInternalServerError, err)
 			return
 		}
+		rpt.UnsafeRemovePartMergedNodes(ctx)
 		req.ParseForm()
 		renderer, filter, err := r.RendererForTopology(topologyID, req.Form, rpt)
 		if err != nil {
diff --git a/app/api_topology.go b/app/api_topology.go
index b6a941ce2..255976216 100644
--- a/app/api_topology.go
+++ b/app/api_topology.go
@@ -182,6 +182,7 @@ func (wc *websocketState) update(ctx context.Context) error {
 	if err != nil {
 		return errors.Wrap(err, "Error generating report")
 	}
+	re.UnsafeRemovePartMergedNodes(ctx)
 	renderer, filter, err := topologyRegistry.RendererForTopology(wc.topologyID, wc.values, re)
 	if err != nil {
 		return errors.Wrap(err, "Error generating report")
diff --git a/app/benchmark_internal_test.go b/app/benchmark_internal_test.go
index 499ce1ed8..da87079d5 100644
--- a/app/benchmark_internal_test.go
+++ b/app/benchmark_internal_test.go
@@ -87,6 +87,7 @@ func getReport(b *testing.B) report.Report {
 
 func benchmarkRender(b *testing.B, f func(report.Report)) {
 	r := getReport(b)
+	r.UnsafeRemovePartMergedNodes(context.Background())
 	b.ResetTimer()
 	for i := 0; i < b.N; i++ {
 		b.StopTimer()
diff --git a/app/collector_test.go b/app/collector_test.go
index 22af88167..f33d4c21e 100644
--- a/app/collector_test.go
+++ b/app/collector_test.go
@@ -23,10 +23,10 @@ func TestCollector(t *testing.T) {
 	defer mtime.NowReset()
 
 	r1 := report.MakeReport()
-	r1.Endpoint.AddNode(report.MakeNode("foo"))
+	r1.Endpoint.AddNode(report.MakeNode("foo").WithTopology("bar"))
 
 	r2 := report.MakeReport()
-	r2.Endpoint.AddNode(report.MakeNode("foo"))
+	r2.Endpoint.AddNode(report.MakeNode("foo").WithTopology("bar"))
 
 	have, err := c.Report(ctx, mtime.Now())
 	if err != nil {
@@ -52,6 +52,7 @@ func TestCollector(t *testing.T) {
 	merged := report.MakeReport()
 	merged.UnsafeMerge(r1)
 	merged.UnsafeMerge(r2)
+	merged.UnsafeRemovePartMergedNodes(context.Background())
 	have, err = c.Report(ctx, mtime.Now())
 	if err != nil {
 		t.Error(err)
diff --git a/report/node.go b/report/node.go
index 859398be0..10f523dfd 100644
--- a/report/node.go
+++ b/report/node.go
@@ -236,3 +236,10 @@ func (n *Node) UnsafeUnMerge(other Node) bool {
 	// metrics don't overlap so just check if we have any
 	return remove && len(n.Metrics) == 0
 }
+
+// If a node is removed from source between two full reports, then we
+// might only have a delta of its last state. Detect that from a blank topology,
+// which cannot arise in a properly-formed Node.
+func (n *Node) isPartMerged() bool {
+	return n.Topology == ""
+}
diff --git a/report/report.go b/report/report.go
index 1534c6803..611f84e98 100644
--- a/report/report.go
+++ b/report/report.go
@@ -1,11 +1,14 @@
 package report
 
 import (
+	"context"
 	"fmt"
 	"math/rand"
 	"strings"
 	"time"
 
+	opentracing "github.com/opentracing/opentracing-go"
+
 	"github.com/weaveworks/scope/common/xfer"
 )
 
@@ -363,6 +366,29 @@ func (r *Report) UnsafeUnMerge(other Report) {
 	})
 }
 
+// UnsafeRemovePartMergedNodes removes nodes that have not fully re-merged.
+// E.g. if a node is removed from source between two full reports, then we
+// might only have a delta of its last state. Remove that from the set.
+// The original is modified.
+func (r *Report) UnsafeRemovePartMergedNodes(ctx context.Context) {
+	dropped := map[string]int{}
+	r.WalkNamedTopologies(func(name string, t *Topology) {
+		for k, v := range t.Nodes {
+			if v.isPartMerged() {
+				delete(t.Nodes, k)
+				dropped[name]++
+			}
+		}
+	})
+	if span := opentracing.SpanFromContext(ctx); span != nil && len(dropped) > 0 {
+		msg := ""
+		for name, count := range dropped {
+			msg += fmt.Sprintf("%s: %d, ", name, count)
+		}
+		span.LogKV("dropped-part-merged", msg)
+	}
+}
+
 // WalkTopologies iterates through the Topologies of the report,
 // potentially modifying them
 func (r *Report) WalkTopologies(f func(*Topology)) {