The package will regenerate all files (conversions) using the saved manipulation as the first manipulation when creating each derived image.
You can also apply media specific manipulations to an existing Media instance.
$mediaItems = $yourModel->getMedia('images');
$mediaItems->manipulations = [
'thumb' => ['orientation' => '90'],
// This will cause the thumb conversions to be regenerated.
First the rotation will be applied for this specific $mediaItem, then the other manipulations you specified in the thumb conversion.
Of course you can also set media specific manipulations for multiple conversions in one go:
Lets take the example again of this one image $mediaItem that needs to be rotated and was linked to $yourModel. Imagine we have a lot of conversions for all the media: thumb, small for web, cmyk for print in full resolution.
Having to add all these manipulation keys with orientation 90 would be a pain.
You can avoid this pain by using a wildcard. Manipulations of the wildcard will be added to each conversion of the media.