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:

