I can understand them wanting to start with the "one year later" thing, because that is a good starting point (and it also is actually one year later from the start of season 1). The problem is that it kind of screws up other things in the timeline.
The first season ended in late fall, early winter, with the ski trip being around that same time (as in the manga timeline they go back to work for a while between the ski trip and Christmas episodes).
Meaning they've skipped ahead in time more than four months. And the explanation given is that they're doing commission work for other teams. Which is fine, but for that long? With no hint of a new project? And with Eagle Jump being a small company, with as far as we know only one other production team. And they're only just now starting to think of using the break in work to play around.
I don't really have a problem with them changing the order of things, but it bothers me when the timeline doesn't make sense. Especially given that the manga has always had a pretty strict timeline.
There were a few places in season 1 where this happened, too.