diff --git a/lib/scripts/lyxpak.py b/lib/scripts/lyxpak.py
index 9d5add137d..cc1bdfda7b 100755
--- a/lib/scripts/lyxpak.py
+++ b/lib/scripts/lyxpak.py
@@ -298,10 +298,9 @@ def main(args):
     # Find the topmost dir common to all files
     if len(incfiles) > 1:
         topdir = os.path.commonprefix(incfiles)
-        # Check whether topdir is valid, as os.path.commonprefix() works on
-        # a character by character basis, rather than on path elements.
-        if not os.path.exists(topdir):
-            topdir = os.path.dirname(topdir) + os.path.sep
+        # As os.path.commonprefix() works on a character by character basis,
+        # rather than on path elements, we need to remove any trailing bytes.
+        topdir = topdir.rpartition(os.path.sep)[0] + os.path.sep
     else:
         topdir = os.path.dirname(incfiles[0]) + os.path.sep