diff --git a/storage/local/crashrecovery.go b/storage/local/crashrecovery.go
index 16950ff300..78e2e0aed3 100644
--- a/storage/local/crashrecovery.go
+++ b/storage/local/crashrecovery.go
@@ -42,6 +42,12 @@ func (p *persistence) recoverFromCrash(fingerprintToSeries map[clientmodel.Finge
 	count := 0
 	seriesDirNameFmt := fmt.Sprintf("%%0%dx", seriesDirNameLen)
 
+	// Delete the fingerprint mapping file as it might be stale or
+	// corrupt. We'll rebuild the mappings as we go.
+	os.Remove(p.mappingsFileName())
+	// The mappings to rebuild.
+	fpm := fpMappings{}
+
 	glog.Info("Scanning files.")
 	for i := 0; i < 1<<(seriesDirNameLen*4); i++ {
 		dirname := path.Join(p.basePath, fmt.Sprintf(seriesDirNameFmt, i))
@@ -58,7 +64,7 @@ func (p *persistence) recoverFromCrash(fingerprintToSeries map[clientmodel.Finge
 				return err
 			}
 			for _, fi := range fis {
-				fp, ok := p.sanitizeSeries(dirname, fi, fingerprintToSeries)
+				fp, ok := p.sanitizeSeries(dirname, fi, fingerprintToSeries, fpm)
 				if ok {
 					fpsSeen[fp] = struct{}{}
 				}
@@ -75,7 +81,7 @@ func (p *persistence) recoverFromCrash(fingerprintToSeries map[clientmodel.Finge
 	for fp, s := range fingerprintToSeries {
 		if _, seen := fpsSeen[fp]; !seen {
 			// fp exists in fingerprintToSeries, but has no representation on disk.
-			if s.headChunkClosed {
+			if s.persistWatermark == len(s.chunkDescs) {
 				// Oops, everything including the head chunk was
 				// already persisted, but nothing on disk.
 				// Thus, we lost that series completely. Clean
@@ -112,17 +118,24 @@ func (p *persistence) recoverFromCrash(fingerprintToSeries map[clientmodel.Finge
 				s.persistWatermark = 0
 				s.chunkDescsOffset = 0
 			}
+			maybeAddMapping(fp, s.metric, fpm)
 			fpsSeen[fp] = struct{}{} // Add so that fpsSeen is complete.
 		}
 	}
 	glog.Info("Check for series without series file complete.")
 
-	if err := p.cleanUpArchiveIndexes(fingerprintToSeries, fpsSeen); err != nil {
+	if err := p.cleanUpArchiveIndexes(fingerprintToSeries, fpsSeen, fpm); err != nil {
 		return err
 	}
 	if err := p.rebuildLabelIndexes(fingerprintToSeries); err != nil {
 		return err
 	}
+	// Finally rewrite the mappings file if there are any mappings.
+	if len(fpm) > 0 {
+		if err := p.checkpointFPMappings(fpm); err != nil {
+			return err
+		}
+	}
 
 	p.setDirty(false)
 	glog.Warning("Crash recovery complete.")
@@ -156,7 +169,9 @@ func (p *persistence) recoverFromCrash(fingerprintToSeries map[clientmodel.Finge
 //   is checked for its presence in the index of archived series. If it cannot
 //   be found there, it is moved into the orphaned directory.
 func (p *persistence) sanitizeSeries(
-	dirname string, fi os.FileInfo, fingerprintToSeries map[clientmodel.Fingerprint]*memorySeries,
+	dirname string, fi os.FileInfo,
+	fingerprintToSeries map[clientmodel.Fingerprint]*memorySeries,
+	fpm fpMappings,
 ) (clientmodel.Fingerprint, bool) {
 	filename := path.Join(dirname, fi.Name())
 	purge := func() {
@@ -222,6 +237,7 @@ func (p *persistence) sanitizeSeries(
 		if s == nil {
 			panic("fingerprint mapped to nil pointer")
 		}
+		maybeAddMapping(fp, s.metric, fpm)
 		if !p.pedanticChecks &&
 			bytesToTrim == 0 &&
 			s.chunkDescsOffset != -1 &&
@@ -320,12 +336,14 @@ func (p *persistence) sanitizeSeries(
 		return fp, false
 	}
 	// This series looks like a properly archived one.
+	maybeAddMapping(fp, metric, fpm)
 	return fp, true
 }
 
 func (p *persistence) cleanUpArchiveIndexes(
 	fpToSeries map[clientmodel.Fingerprint]*memorySeries,
 	fpsSeen map[clientmodel.Fingerprint]struct{},
+	fpm fpMappings,
 ) error {
 	glog.Info("Cleaning up archive indexes.")
 	var fp codable.Fingerprint
@@ -359,7 +377,12 @@ func (p *persistence) cleanUpArchiveIndexes(
 			_, err := p.archivedFingerprintToTimeRange.Delete(fp)
 			return err
 		}
-		// fp is legitimately archived. Make sure it is in timerange index, too.
+		// fp is legitimately archived. Now we need the metric to check for a mapped fingerprint.
+		if err := kv.Value(&m); err != nil {
+			return err
+		}
+		maybeAddMapping(clientmodel.Fingerprint(fp), clientmodel.Metric(m), fpm)
+		// Make sure it is in timerange index, too.
 		has, err := p.archivedFingerprintToTimeRange.Has(fp)
 		if err != nil {
 			return err
@@ -372,9 +395,6 @@ func (p *persistence) cleanUpArchiveIndexes(
 		if _, err := p.archivedFingerprintToMetrics.Delete(fp); err != nil {
 			return err
 		}
-		if err := kv.Value(&m); err != nil {
-			return err
-		}
 		series := newMemorySeries(clientmodel.Metric(m), false, clientmodel.Earliest)
 		cds, err := p.loadChunkDescs(clientmodel.Fingerprint(fp), clientmodel.Now())
 		if err != nil {
@@ -455,3 +475,20 @@ func (p *persistence) rebuildLabelIndexes(
 	glog.Info("All requests for rebuilding the label indexes queued. (Actual processing may lag behind.)")
 	return nil
 }
+
+// maybeAddMapping adds a fingerprint mapping to fpm if the FastFingerprint of m is different from fp.
+func maybeAddMapping(fp clientmodel.Fingerprint, m clientmodel.Metric, fpm fpMappings) {
+	if rawFP := m.FastFingerprint(); rawFP != fp {
+		glog.Warningf(
+			"Metric %v with fingerprint %v is mapped from raw fingerprint %v.",
+			m, fp, rawFP,
+		)
+		if mappedFPs, ok := fpm[rawFP]; ok {
+			mappedFPs[metricToUniqueString(m)] = fp
+		} else {
+			fpm[rawFP] = map[string]clientmodel.Fingerprint{
+				metricToUniqueString(m): fp,
+			}
+		}
+	}
+}
diff --git a/storage/local/persistence.go b/storage/local/persistence.go
index f26ac76fbc..7b2a34cecd 100644
--- a/storage/local/persistence.go
+++ b/storage/local/persistence.go
@@ -1418,7 +1418,7 @@ loop:
 // (4.3.1) The uvarint-encoded length of the unique metric string.
 // (4.3.2) The unique metric string.
 // (4.3.3) The mapped fingerprint as big-endian uint64.
-func (p *persistence) checkpointFPMappings(c fpMappings) (err error) {
+func (p *persistence) checkpointFPMappings(fpm fpMappings) (err error) {
 	glog.Info("Checkpointing fingerprint mappings...")
 	begin := time.Now()
 	f, err := os.OpenFile(p.mappingsTempFileName(), os.O_WRONLY|os.O_TRUNC|os.O_CREATE, 0640)
@@ -1449,11 +1449,11 @@ func (p *persistence) checkpointFPMappings(c fpMappings) (err error) {
 	if _, err = codable.EncodeUvarint(w, mappingsFormatVersion); err != nil {
 		return
 	}
-	if _, err = codable.EncodeUvarint(w, uint64(len(c))); err != nil {
+	if _, err = codable.EncodeUvarint(w, uint64(len(fpm))); err != nil {
 		return
 	}
 
-	for fp, mappings := range c {
+	for fp, mappings := range fpm {
 		if err = codable.EncodeUint64(w, uint64(fp)); err != nil {
 			return
 		}