diff --git a/docs/developer-guide.md b/docs/developer-guide.md
index b258af43..4617c062 100644
--- a/docs/developer-guide.md
+++ b/docs/developer-guide.md
@@ -397,7 +397,7 @@ class BootstrapGenerator:
 - `_render_template()` — Render Jinja2 template with context variables
 - `_get_templates_for_language()` — Map language to template files
 - `_write_file()` — Create file on disk (respects dry_run)
-- `_file_exists()` — Check for conflicts (never overwrites)
+- `_write_file()` — Write file to disk (⚠️ currently overwrites existing files, see [#449](https://github.com/ambient-code/agentready/issues/449))
 
 #### 2. Bootstrap CLI (`cli/bootstrap.py`)
 
diff --git a/docs/user-guide.md b/docs/user-guide.md
index 7b8b8178..0bb7b19c 100644
--- a/docs/user-guide.md
+++ b/docs/user-guide.md
@@ -98,7 +98,7 @@ Bootstrap is AgentReady's automated infrastructure generator. One command create
 **Safe by Design**:
 
 - Use `--dry-run` to preview changes
-- Never overwrites existing files
+- Never overwrites existing files (⚠️ [not yet fully implemented](https://github.com/ambient-code/agentready/issues/449), currently only `CONTRIBUTING.md` and `CODE_OF_CONDUCT.md` are protected)
 - Review with `git status` before committing
 
 ### When to Use Bootstrap vs Assess