In the comments section of the below link, there is a workaround provided to overcome the limitation.
https://dev.mysql.com/doc/refman/5.0/en/innodb-auto-increment-handling.html
*As InnoDb forgets its highest auto_increment after server restart, you can set it again, if you have stored it anywhere. This happens often if you archive your data in an archive table and then delete it and then restart mysql. When archiving again this will result in duplicate key entries. To work around this you can create a trigger which makes sure your auto_increment is higher than the auto_increment of your archive table:*
delimiter //
drop trigger if exists trigger_autoinc_tbl;
CREATE TRIGGER trigger_autoinc_tbl BEFORE INSERT ON tbl
FOR EACH ROW
BEGIN
declare auto_incr1 BIGINT;
declare auto_incr2 BIGINT;
SELECT AUTO_INCREMENT INTO auto_incr1 FROM information_schema.TABLES WHERE table_schema=DATABASE() AND table_name='tbl';
SELECT AUTO_INCREMENT INTO auto_incr2 FROM information_schema.TABLES WHERE table_schema=DATABASE() AND table_name='tbl_archiv';
IF (auto_incr2 > auto_incr1 and NEW.id<auto_incr2) THEN
SET NEW.id = auto_incr2;
END IF;
END;//
delimiter ;