As Jon mentioned, I would use GUIDs to solve the merge task. And I see two different solutions that required GUIDs:
1) Permanently change your database schema to use GUIDs instead of INTEGER (IDENTITY) as primary key.
This is a good solution in general, but if you have a lot of non SQL code that is somehow bound to the way your identifiers work, it could require quite some code changes. Probably since you merge databases, you may anyways need to update your application so that it is working with one region data only based on the user logged in etc.
2) Temporarily add GUIDs for migration purposes only, and after the data is migrated, drop them:
This one is kind-of more tricky, but once you write this migration script, you can (re-)run it multiple times to merge databases again in case you screw it the first time. Here is an example:
Table: PERSON (ID INT PRIMARY KEY, Name VARCHAR(100) NOT NULL)
Table: ADDRESS (ID INT PRIMARY KEY, City VARCHAR(100) NOT NULL, PERSON_ID INT)
Your alter scripts are (note that for all PK we automatically generate the GUID):
ALTER TABLE PERSON ADD UID UNIQUEIDENTIFIER NOT NULL DEFAULT (NEWID())
ALTER TABLE ADDRESS ADD UID UNIQUEIDENTIFIER NOT NULL DEFAULT (NEWID())
ALTER TABLE ADDRESS ADD PERSON_UID UNIQUEIDENTIFIER NULL
Then you update the FKs to be consistent with INTEGER ones:
--// set ADDRESS.PERSON_UID
UPDATE ADDRESS
SET ADDRESS.PERSON_UID = PERSON.UID
FROM ADDRESS
INNER JOIN PERSON
ON ADDRESS.PERSON_ID = PERSON.ID
You do this for all PKs (automatically generate GUID) and FKs (update as shown above).
Now you create your target database. In this target database you also add the UID columns for all the PKs and FKs. Also disable all FK constraints.
Now you insert from each of your source databases to the target one (note: we do not insert PKs and integer FKs):
INSERT INTO TARGET_DB.dbo.PERSON (UID, NAME)
SELECT UID, NAME FROM SOURCE_DB1.dbo.PERSON
INSERT INTO TARGET_DB.dbo.ADDRESS (UID, CITY, PERSON_UID)
SELECT UID, CITY, PERSON_UID FROM SOURCE_DB1.dbo.ADDRESS
Once you inserted data from all the databases, you run the code opposite to the original to make integer FKs consistent with GUIDs on the target database:
--// set ADDRESS.PERSON_ID
UPDATE ADDRESS
SET ADDRESS.PERSON_ID = PERSON.ID
FROM ADDRESS
INNER JOIN PERSON
ON ADDRESS.PERSON_UID = PERSON.UID
Now you may drop all the UID columns:
ALTER TABLE PERSON DROP COLUMN UID
ALTER TABLE ADDRESS DROP COLUMN UID
ALTER TABLE ADDRESS DROP COLUMN PERSON_UID
So at the end you should get a rather long migration script, that should do the job for you. The point is - IT IS DOABLE
NOTE: all written here is not tested.