--- a/mesonbuild/compilers/compilers.py
+++ b/mesonbuild/compilers/compilers.py
@@ -1112,6 +1112,8 @@
         for p in rpath_paths:
             if p == from_dir:
                 relative = '' # relpath errors out in this case
+            elif os.path.isabs(p):
+                relative = p # These can be outside of build dir.
             else:
                 relative = os.path.relpath(os.path.join(build_dir, p), os.path.join(build_dir, from_dir))
             rel_rpaths.append(relative)
@@ -1121,8 +1123,10 @@
             if paths != '':
                 paths += ':'
             paths += build_rpath
-        if len(paths) < len(install_rpath):
-            padding = 'X' * (len(install_rpath) - len(paths))
+        store_paths = ':'.join(filter(lambda path: path.startswith('@storeDir@'), paths.split(':')))
+        extra_space_needed = len(install_rpath + (':' if install_rpath and store_paths else '') + store_paths) - len(paths)
+        if extra_space_needed > 0:
+            padding = 'X' * extra_space_needed
             if not paths:
                 paths = padding
             else:
--- a/mesonbuild/scripts/depfixer.py
+++ b/mesonbuild/scripts/depfixer.py
@@ -303,6 +303,14 @@
             return
         self.bf.seek(rp_off)
         old_rpath = self.read_str()
+
+        if new_rpath:
+            new_rpath += b':'
+        else:
+            new_rpath = b''
+
+        new_rpath += b':'.join(filter(lambda path: path.startswith(b'@storeDir@'), old_rpath.split(b':')))
+
         if len(old_rpath) < len(new_rpath):
             sys.exit("New rpath must not be longer than the old one.")
         # The linker does read-only string deduplication. If there is a
@@ -316,6 +324,10 @@
         if not new_rpath:
             self.remove_rpath_entry(entrynum)
         else:
+            # clean old rpath to avoid stale references
+            # (see https://github.com/NixOS/nixpkgs/pull/46020)
+            self.bf.seek(rp_off)
+            self.bf.write(b'\0'*len(old_rpath))
             self.bf.seek(rp_off)
             self.bf.write(new_rpath)
             self.bf.write(b'\0')