Set all boolean certain fields to 0 if 1 with rules
To clarify, you have created a new flag using the Flag module and attached it to a taxonomy bundle (either terms or vocabularies) and want to reset these flags. 

You can do this directly in your database with a couple commands. First, you need the Flag ID of your flag which is in the 'flags' table:

mysql&gt; desc flags;
+--------------+----------------------+------+-----+---------+----------------+
| Field        | Type                 | Null | Key | Default | Extra          |
+--------------+----------------------+------+-----+---------+----------------+
| fid          | smallint(5) unsigned | NO   | PRI | NULL    | auto_increment |
| content_type | varchar(32)          | NO   |     |         |                |
| name         | varchar(128)         | YES  | UNI |         |                |
| title        | varchar(255)         | YES  |     |         |                |
| global       | tinyint(4)           | YES  |     | 0       |                |
| options      | text                 | YES  |     | NULL    |                |
+--------------+----------------------+------+-----+---------+----------------+


You can find this by selecting the fid, and name from flags:

mysql&gt; select fid, name from flags;
+-----+---------------+
| fid | name          |
+-----+---------------+
|   1 | bookmarks     |
|   3 | taxonomy_flag |
+-----+---------------+


In my development server, the taxonomy_flag id is 3. Now take a look at the flag_content table where all the flag content data is stored:

mysql&gt; desc flag_content;
+--------------+----------------------+------+-----+---------+----------------+
| Field        | Type                 | Null | Key | Default | Extra          |
+--------------+----------------------+------+-----+---------+----------------+
| fcid         | int(10) unsigned     | NO   | PRI | NULL    | auto_increment |
| fid          | smallint(5) unsigned | NO   | MUL | 0       |                |
| content_type | varchar(128)         | NO   | MUL |         |                |
| content_id   | int(10) unsigned     | NO   | MUL | 0       |                |
| uid          | int(10) unsigned     | NO   |     | 0       |                |
| sid          | int(10) unsigned     | NO   |     | 0       |                |
| timestamp    | int(10) unsigned     | NO   |     | 0       |                |
+--------------+----------------------+------+-----+---------+----------------+


What you want to do to reset all the values for your target flag is delete all entries from the flag_content table, so in my example above that would be 

delete from flag_content where fid=3;