The collation determines how results are sorted and ordered. In newer versions of Atlassian applications, collation changes may become more strict - i.e, an application requires a certain collation. You must ensure your database has the correct collation for the application it will be used with.
Additionally, the information inside a column may be encoded incorrectly as well - causing the data in that column to be displayed incorrectly.
You may wish to add all the ALTER TABLE statements to a single file for easier execution.
It may be necessary to ignore foreign key constraints when making changes to a large number of columns. You can use the SET FOREIGN_KEY_CHECKS command to ignore foreign key constraints while you update the database.