You could write a script to update the FK's for you.. check out this blog: http://multunus.com/2011/03/how-to-easily-merge-two-identical-mysql-databases/
They have a clever script to use the information_schema tables to get the "id" columns:
SET @db:='id_new';
select @max_id:=max(AUTO_INCREMENT) from information_schema.tables;
select concat('update ',table_name,' set ', column_name,' = ',column_name,'+',@max_id,' ; ') from information_schema.columns where table_schema=@db and column_name like '%id' into outfile 'update_ids.sql';
use id_new
source update_ids.sql;
It depends on the semantic of the primary key. If it's just autoincrement, then use something like:
insert into table1 (all columns except pk)
select all_columns_except_pk
from table2;
If PK means something, you need to find a way to determine which record should have priority. You could create a select query to find duplicates first (see answer by cpitis). Then eliminate the ones you don't want to keep and use the above insert to add records that remain.
If you need to do it manually, one time:
First, merge in a temporary table, with something like:
create table MERGED as select * from table 1 UNION select * from table 2
Then, identify the primary key constraints with something like
SELECT COUNT(*), PK from MERGED GROUP BY PK HAVING COUNT(*) > 1
Where PK is the primary key field...
Solve the duplicates.
Rename the table.
[edited - removed brackets in the UNION query, which was causing the error in the comment below]
INSERT
INTO first_table f
SELECT *
FROM second_table s
ON DUPLICATE KEY
UPDATE
s.column1 = DO_WHAT_EVER_MUST_BE_DONE_ON_KEY_CLASH(f.column1)
Not as complicated as it sounds.... Just leave the duplicate primary key out of your query.... this works for me !
INSERT INTO
Content(
`status`,
content_category,
content_type,
content_id,
user_id,
title,
description,
content_file,
content_url,
tags,
create_date,
edit_date,
runs
)
SELECT `status`,
content_category,
content_type,
content_id,
user_id,
title,
description,
content_file,
content_url,
tags,
create_date,
edit_date,
runs
FROM
Content_Images
Source: Stackoverflow.com