I think that Ash and Nurse Joy finds the Stoutland under the bridge where it was last and they carefully picked it up and took it back to the Pokemon center without waking up Litten. The Stoutland died shortly after arriving to the Pokemon center the second time.
It's a great episode, and it's also sad that Stoutland passed away and watching Litten going through through it. Stoutland will watch Litten from heaven, watching him grow stronger with Ash.
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