I had FCP do something similar to this in a 25F/48K workflow. Three
months after I delivered the final mix of a documentary I recieved a
call from the editor saying the final mix was not lining up anymore.
The editor was working off of a copy of the original master session in
FCP prepping to send it to a post house in Europe for Foreign language
versions. When the copy was made, FCP was interpreting my final mix
as a pull down and changed the length. I uploaded a wav and aiff
version of the mix again and both didn't line up. We checked the
original edit system and everything was fine. FCP was just doing this
pull down on the copy. To solve the problem we time stretched the
audio back. Fortunately, there wasn't any audible problems.
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