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Searching for a film name here, or possibly a TV miniseries. Plotline: aliens came to visit Earth and stayed, generously offering their travel technology to us humans. I think it was aired in the mid- to late 1990s.

With teleporting stations around everywhere and accessible to near everyone, travel times were shortened to mere minutes per trip, over any earthly distance. This clean technology revolutionized the world. Soon, humanity couldn't live without, it helped solve so many problems.

Only a few sceptical humans investigated, because both they wondered "why would aliens do this without apparent benefit for themselves", and the apparent lag between 'going in' and 'coming out the other end', which was considerable, a few minutes IIRC. In-universe, the lag was explained away as a technical issue. These humans found the aliens were indeed doing just what you'd need to do: collect all information about a given traveller, down to molecule and atom excitement level, and sending all of it to be replicated at the far end - but aliens were also thoroughly investigating what they had before reproducing it. Possibly they were also altering the copy ever so slightly how they saw fit.

They may have also not deleted the copied data they had. (Not perfectly sure about this last aspect.)

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"Earth: Final Conflict" was a science fiction series which ran over 5 series from 1997 to 2001. Based on concepts developed by Gene Roddenberry, it dealt with the arrival of an alien race, the Taelons, on Earth. Episode 19 of season 1, "Through the Looking Glass" seems to describe the situation in the question. From tvtropes:

New portal stations are open that allow rapid transportation between Los Angeles and New York in ten minutes. Passengers are kept in stasis to protect them during the trip through ID space... The Resistance sends in Sahjit with a way to keep him from being kept in stasis. He learns that all passengers arrive to the Taelon base on the far side of the Moon, where experiments are performed on them while they're unconscious, at which point they're sent to their destination.

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    Aw man... I saw several references to that show when I searched, but all referencing the human modifications of it. Good job!
    – FuzzyBoots
    Oct 5 at 20:25
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    Thank you very much! That was the one. That it is Gene Roddenberry related had completely escaped my attention now..
    – raddaqii
    Oct 6 at 5:57

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