I am having this same issue, did you every figure something out to make it work?
Yes: I edited the .smodel (json) file in a text editor. I found all my source tables in the json, cut+pasted their json to sit under a single dataset, and deleted the now-empty other data sources.
Be careful: it's easy to corrupt the .smodel if you make a mistake in the json. But it's also easy to avoid that risk: (a) Download a backup of your .smodel. (b) When you upload, create a new model rather than overwriting. Make sure the model builds and check that a few tables have data, maybe even run a few widgets off it. If it works, then you can commit to it.
Tip: A dedicated json editor might let you drag-and-drop the tables and delete datasets more quickly and without risk of corrupting. But I was ok just using notepad.
