Where is the CCK autocomplete widget field php configuration code stored?
Try looking in the content_node_field table, under the global settings value:

mysql&gt; desc content_node_field;
+-----------------+--------------+------+-----+---------+-------+
| Field           | Type         | Null | Key | Default | Extra |
+-----------------+--------------+------+-----+---------+-------+
| field_name      | varchar(32)  | NO   | PRI |         |       |
| type            | varchar(127) | NO   |     |         |       |
| global_settings | mediumtext   | NO   |     | NULL    |       |
| required        | tinyint(4)   | NO   |     | 0       |       |
| multiple        | tinyint(4)   | NO   |     | 0       |       |
| db_storage      | tinyint(4)   | NO   |     | 1       |       |
| module          | varchar(127) | NO   |     |         |       |
| db_columns      | mediumtext   | NO   |     | NULL    |       |
| active          | tinyint(4)   | NO   |     | 0       |       |
| locked          | tinyint(4)   | NO   |     | 0       |       |
+-----------------+--------------+------+-----+---------+-------+


I just did a test, defining an arbitrary PHP string (print "Hello Stack Exchange";) under allowed values for a field (field_test2) and found the following: 

mysql&gt; select global_settings from content_node_field where field_name = "field_test2";

+----------------------------------------------------------------------------------------------------------------------------------------------------+
| global_settings                                                                                                                                    |
+----------------------------------------------------------------------------------------------------------------------------------------------------+
| a:4:{s:15:"text_processing";s:1:"0";s:10:"max_length";s:0:"";s:14:"allowed_values";s:0:"";s:18:"allowed_values_php";s:31:"print "Hello Stack Exchange";";} |
+----------------------------------------------------------------------------------------------------------------------------------------------------+


The string you are looking for is at the end (s:31:"print "Hello Stack Exchange";";) and it's serialized with the character count at the front. If you want to zero this out, it would look like: 

a:4:{s:15:"text_processing";s:1:"0";s:10:"max_length";s:0:"";s:14:"allowed_values";s:0:"";s:18:"allowed_values_php";s:0:"";}