I'd guess that, along with converting all of their artwork to bitmaps, this was needed because Haxe+OpenFL didn't support what they were doing before. If they were going to have to change it anyway better to make that change before the port so you don't mix up two sets of bugs.
This makes a lot of sense. Doing a major refactoring while migrating to a new language/platform is much harder than refactoring a codebase so that it more closely mimics a line by line translation to a new language, and then doing the line by line translation. It may look like more work, especially since you are almost guaranteed to touch the same code twice, but the the cognitive load is so much lower each time, that the extra effort will make it all so much easier.
