In my case, I can stay in the lab of my major project after I finished my internship (NKI). Then I will help my supervisor with a different project, so a different topic then my major research project. I will stay to do some experiments and help with writing the article. No new students are accepted in the NKI until January, so the problem of taking someones spot is not the case.
Yes, it is possible to do a mini-project in the same external institute as your research project, as long as the topic, and therefore the references in the final product do not have significant overlap.
Please, make sure to include a statement from your examiner (explaining the differences between the two projects) together with the submission of your application form.
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