If you have your Program set up as a Multi-List View under Enrollment Period, like this:
Then you will also have "Class Selection Lists" like this (except your lists will be named something different, of course):
You can reorder the Class Selection List here by following these steps:
On the Programs page, click the pencil icon beside the Program
In the program editor, click on "Enrollment Model" on the left menu
Scroll down to the "Class Selection Lists" block (see screenshot above).
Click on "Add/Remove selection list"
Click and hold the dots beside the Class Selection and drag the selection to move it to another order
Click off the window to close it
Be sure to click "Save" to save the changes made
The above steps will have to be done for EACH Program you need to change the Class Selection Lists for. This cannot be done in bulk.