From what I recall, the APM now handles this intelligently. It should run any scripts with a starting number GREATER THAN OR EQUAL to your current version AND an ending number LESS THAN OR EQUAL to your desired version (i.e. the version currently in the .info file of the package you're upgrading). So, as an example, if you're currently at version 4.0.1 and the version-number in the .info file is 4.4, the APM would run upgrade-4.0.1-4.1.sql, then upgrade-4.1-4.3.sql and then upgrade-4.3-4.3.2a.sql, but never upgrade-4.0-4.0.1.sql.
