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I agree with ratbastid. You mention that the company has a high retention rate, but you don't want to work in that line for long. So that's not much of an advantage in the end.
You will very likely be able to interview again in the future for research positions similar to the one you are offered. However the start-up where you get to be chief engineer seems to be a less frequent proposition, and yes it's a gamble.. But it could pay off big; in the worst case you can always use your experience and get another job if this doesn't work out.
But I certainly understand your doubts, with the funding being flaky. It's a tough one. Good luck.
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