Transferring the data wouldn't be a problem, if you completely specify the auto_increment values. MySQL allows you to insert anything you want into an auto_increment field, but only does the actual auto_increment if the value you're inserting is 0 or NULL. At least on my 5.0 copy of MySQL, it'll automatically adjust the auto_increment value to take into account what you've inserted:
mysql> create table test (x int auto_increment primary key);
Query OK, 0 rows affected (0.01 sec)
mysql> insert into test (x) values (10);
Query OK, 1 row affected (0.00 sec)
mysql> insert into test (x) values (null);
Query OK, 1 row affected (0.00 sec)
mysql> insert into test (x) values (0);
Query OK, 1 row affected (0.00 sec)
mysql> insert into test (x) values (5);
Query OK, 1 row affected (0.00 sec)
mysql> select * from test;
+----+
| x |
+----+
| 5 | <--inserted '5' (#4)
| 10 | <--inserted '10' (#1)
| 11 | <--inserted 'null' (#2)
| 12 | <--inserted '0' (#3)
+----+
3 rows in set (0.00 sec)
You can also adjust the table's next auto_increment value as follows:
mysql> alter table test auto_increment=500;
Query OK, 4 rows affected (0.04 sec)
Records: 4 Duplicates: 0 Warnings: 0
mysql> insert into test (x) values (null);
Query OK, 1 row affected (0.00 sec)
mysql> select last_insert_id();
+------------------+
| last_insert_id() |
+------------------+
| 500 |
+------------------+
1 row in set (0.01 sec)