diff --git a/scripts/nix-channel.in b/scripts/nix-channel.in
index 19b012922..e3abc7ea5 100644
--- a/scripts/nix-channel.in
+++ b/scripts/nix-channel.in
@@ -23,6 +23,7 @@ sub readChannels {
     open CHANNELS, "<$channelsList" or die "cannot open `$channelsList': $!";
     while (<CHANNELS>) {
         chomp;
+        next if /^\s*\#/;
         push @channels, $_;
     }
     close CHANNELS;
@@ -81,7 +82,7 @@ sub update {
     # Pull cache manifests.
     foreach my $url (@channels) {
         print "pulling cache manifest from `$url'\n";
-        system("@bindir@/nix-pull", "$url/MANIFEST") == 0
+        system("@bindir@/nix-pull", "--skip-wrong-store", "$url/MANIFEST") == 0
             or die "cannot pull cache manifest from `$url'";
     }
 
diff --git a/scripts/nix-pull.in b/scripts/nix-pull.in
index 0af036f6f..c7c20fb9b 100644
--- a/scripts/nix-pull.in
+++ b/scripts/nix-pull.in
@@ -21,6 +21,9 @@ $libexecDir = "@libexecdir@" unless defined $libexecDir;
 my $stateDir = $ENV{"NIX_STATE_DIR"};
 $stateDir = "@localstatedir@/nix" unless defined $stateDir;
 
+my $storeDir = $ENV{"NIX_STORE_DIR"};
+$storeDir = "@storedir@" unless defined $storeDir;
+
 
 # Prevent access problems in shared-stored installations.
 umask 0022;
@@ -31,6 +34,8 @@ my %narFiles;
 my %patches;
 my %successors;
 
+my $skipWrongStore = 0;
+
 sub processURL {
     my $url = shift;
 
@@ -45,6 +50,15 @@ sub processURL {
         die "manifest `$url' is too old (i.e., for Nix <= 0.7)\n";
     }
 
+    if ($skipWrongStore) {
+        foreach my $path (keys %narFiles) {
+            if (substr($path, 0, length($storeDir) + 1) ne "$storeDir/") {
+                print STDERR "warning: manifest `$url' assumes a Nix store at a different location than $storeDir, skipping...\n";
+                exit 0;
+            }
+        }
+    }
+
     my $baseName = "unnamed";
     if ($url =~ /\/([^\/]+)\/[^\/]+$/) { # get the forelast component
         $baseName = $1;
@@ -62,7 +76,11 @@ sub processURL {
 
 while (@ARGV) {
     my $url = shift @ARGV;
-    processURL $url;
+    if ($url eq "--skip-wrong-store") {
+        $skipWrongStore = 1;
+    } else {
+        processURL $url;
+    }
 }