diff --git a/Dfm.go b/Dfm.go
index b987234..ac659bc 100644
--- a/Dfm.go
+++ b/Dfm.go
@@ -461,8 +461,8 @@ func (dfm *Dfm) EjectFiles(inputFilenames []string, errorHandler ErrorHandler) e
 func (dfm *Dfm) autoclean(nextManifest map[string]bool) {
 	var toRemove []string
 	for filename := range dfm.Config.manifest {
-		_, found := nextManifest[filename]
-		if !found {
+		_, needed := nextManifest[filename]
+		if !needed {
 			toRemove = append(toRemove, filename)
 		}
 	}
@@ -476,7 +476,7 @@ func (dfm *Dfm) autoclean(nextManifest map[string]bool) {
 			}
 		}
 		dfm.log(OperationRemove, filename, "", err)
-		if err == nil {
+		if err == nil || os.IsNotExist(err) {
 			delete(dfm.Config.manifest, filename)
 		}
 	}
diff --git a/testdata/TestDfm/missing-link.sh b/testdata/TestDfm/missing-link.sh
new file mode 100644
index 0000000..9373aaf
--- /dev/null
+++ b/testdata/TestDfm/missing-link.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+# Tests dfm correctly handling a file that has been unlinked behind dfm's back.
+set -e
+. "$(dirname "$0")/../helpers.sh"
+
+export HOME="$(pwd)/home"
+export DFM_DIR="$HOME/dfmdir"
+
+mkdir -p ~/dfmdir/files
+echo 'config' > ~/dfmdir/files/.bashrc
+
+dfm init --repos files
+dfm link
+
+rm ~/.bashrc
+rm ~/dfmdir/files/.bashrc
+dfm link
+dfm link # no output on second run
diff --git a/testdata/TestDfm/missing-link.sh.snap b/testdata/TestDfm/missing-link.sh.snap
new file mode 100644
index 0000000..0818cf8
--- /dev/null
+++ b/testdata/TestDfm/missing-link.sh.snap
@@ -0,0 +1,7 @@
+$ dfm init --repos files
+Initialized /test/home/dfmdir as a dfm directory.
+$ dfm link
+files/.bashrc -> /test/home/.bashrc
+$ dfm link
+removed .bashrc
+$ dfm link