--- a/mesonbuild/linkers.py
+++ b/mesonbuild/linkers.py
@@ -527,8 +527,10 @@ class GnuLikeDynamicLinkerMixin:
         # In order to avoid relinking for RPATH removal, the binary needs to contain just
         # enough space in the ELF header to hold the final installation RPATH.
         paths = ':'.join(all_paths)
-        if len(paths) < len(install_rpath):
-            padding = 'X' * (len(install_rpath) - len(paths))
+        store_paths = ':'.join(filter(lambda path: path.startswith('@storeDir@'), all_paths))
+        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:
@@ -902,8 +904,10 @@ class SolarisDynamicLinker(PosixDynamicLinkerMixin, DynamicLinker):
         # In order to avoid relinking for RPATH removal, the binary needs to contain just
         # enough space in the ELF header to hold the final installation RPATH.
         paths = ':'.join(all_paths)
-        if len(paths) < len(install_rpath):
-            padding = 'X' * (len(install_rpath) - len(paths))
+        store_paths = ':'.join(filter(lambda path: path.startswith('@storeDir@'), all_paths))
+        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 @@ class Elf(DataSizes):
             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 @@ class Elf(DataSizes):
         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')