diff --git a/scripts/make_generated_files.py b/scripts/make_generated_files.py
index cd60b087f..42b7a7c54 100755
--- a/scripts/make_generated_files.py
+++ b/scripts/make_generated_files.py
@@ -24,10 +24,11 @@ class GenerationScript:
     """
     Representation of a script generating a configuration independent file.
     """
-    # pylint: disable=too-few-public-methods
+    # pylint: disable=too-few-public-methods,too-many-arguments
     def __init__(self, script: Path, files: List[Path],
                  output_dir_option: Optional[str] = None,
-                 output_file_option: Optional[str] = None):
+                 output_file_option: Optional[str] = None,
+                 optional: bool = False):
         # Path from the root of Mbed TLS or TF-PSA-Crypto of the generation script
         self.script = script
 
@@ -49,6 +50,12 @@ class GenerationScript:
         # positional argument.
         self.output_file_option = output_file_option
 
+        # Optional files are skipped in --check mode if they don't exist.
+        # This normally shouldn't happen, but it can happen during transition
+        # periods where we're adding a new script or a new file, and a
+        # consuming repository hasn't been updated yet.
+        self.optional = optional
+
 def get_generation_script_files(generation_script: str):
     """
     Get the list of the default paths of the files that a given script
@@ -77,7 +84,8 @@ if os.path.exists("scripts/generate_config_checks.py"):
     COMMON_GENERATION_SCRIPTS.append(GenerationScript(
         Path("scripts/generate_config_checks.py"),
         get_generation_script_files("scripts/generate_config_checks.py"),
-        "", None))
+        output_dir_option="",
+        optional=True))
 
 if build_tree.looks_like_tf_psa_crypto_root("."):
     TF_PSA_CRYPTO_GENERATION_SCRIPTS = [
@@ -205,6 +213,15 @@ def check_generated_files(generation_scripts: List[GenerationScript], root: Path
     for generation_script in generation_scripts:
         for file in generation_script.files:
             file = root / file
+            if not file.exists():
+                # If the script is just being added, allow its files not
+                # to exist. This can happen, at least, when adding a new
+                # generation script in crypto: until mbedtls is updated,
+                # the files from that script won't be present when
+                # the updated crypto is built from mbedtls development.
+                if generation_script.optional:
+                    continue
+                raise Exception(f"Expected generated file does not exist: {file}")
             bak_file = file.with_name(file.name + ".bak")
             if bak_file.exists():
                 bak_file.unlink()
@@ -222,6 +239,10 @@ def check_generated_files(generation_scripts: List[GenerationScript], root: Path
         for file in generation_script.files:
             file = root / file
             bak_file = file.with_name(file.name + ".bak")
+            if generation_script.optional and not bak_file.exists():
+                # This file is optional and didn't exist before, so
+                # there's nothing to compare to, or clean up.
+                continue
             if not filecmp.cmp(file, bak_file):
                 ref_file = file.with_name(file.name + ".ref")
                 ref_file = root / ref_file
diff --git a/scripts/mbedtls_framework/config_checks_generator.py b/scripts/mbedtls_framework/config_checks_generator.py
index 40b720e45..f55c061cb 100644
--- a/scripts/mbedtls_framework/config_checks_generator.py
+++ b/scripts/mbedtls_framework/config_checks_generator.py
@@ -208,6 +208,17 @@ def generate_header_files(branch_data: BranchData,
 
 def main(branch_data: BranchData) -> None:
     root = build_tree.guess_project_root()
+    # Is root the current directory? The safe default is no, so compare
+    # the paths, rather than calling `os.samefile()` which can have false
+    # positives and can fail in edge cases.
+    if root == os.getcwd():
+        # Be nice and use a relative path when it's simple to do so.
+        # (build_tree.guess_project_root() should probably do this, actually.)
+        # This is not only nice to humans, but also necessary for
+        # `make_generated_files.py --root DIR --check`: it calls
+        # this script with `--list` and expects a path that is relative
+        # to DIR, not an absolute path that is under the project root.
+        root = os.curdir
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument('--list', action='store_true',
                         help='List generated files and exit')