Why does SEG-Y Loader tell me I have a duplicate survey even though the coordinates are not the same?
In general, a survey simply defines the relationship between Inline/Crossline and Eastings/Northings.
Any given survey can be defined by an infinite number of orthogonal tie point sets, so long as they define the same relationship in the conversion from IL/CL to X/Y.
The following example shows two tie point sets that has different coordinates but describe exactly the same relationship between IL/CL and X/Y - and therefore are duplicate surveys:
This is why you receive the "duplicate survey" warning (image below). Even though the tie points sets are different, they define the same relationship as the existing survey, and hence it is labeled as a duplicate.