OK I have added a relation to an existing DataObject with records. The relation is displayed in the CMS through a DropdownField.
I have set the default value for this relation for new records using populateDefaults(), say to 3.

The problem I am having how would I change the default value for records that existed before I added this relationship (as they show up as blank in the GridField and with an ID of 0 in the database for the relationID column).

I can edit the database directly and update all records with ID 0 but an solution coded in the dataobject would be preferable, if this is possible? I also don't want to ask my editors to re-save all records one by one.

Running a SQL query directly would be less code (and faster) but if you want to do it via the framework one way to do migrations is to use a BuildTask.

<?php

class DoStuff extends BuildTask() {

public function run($request) {
$records = Page::get('Page')->filter(array(
"SomeID" => 0
));

foreach($records as $record) {
$record->SomeID = 3;
$record->write();
}

}

Then run dev/tasks/DoStuff to perform the operation.

Ah great hadn't used build tasks before, this example is just what I need to get to grips with that also. Thanks so much Willr!