Remove the ~, comment the lines instead

synapse/config/captcha.py

@@ -47,5 +47,5 @@ class CaptchaConfig(Config):
         captcha_ip_origin_is_x_forwarded: False
 
         # A secret key used to bypass the captcha test entirely.
-        captcha_bypass_secret: ~
+        #captcha_bypass_secret: "YOUR_SECRET_HERE"
         """

synapse/config/server.py

@@ -83,7 +83,7 @@ class ServerConfig(Config):
 
         # Turn on the twisted telnet manhole service on localhost on the given
         # port.
-        manhole: ~
+        #manhole: 9000
         """ % locals()
 
     def read_arguments(self, args):