Hi,
I would split loading the fiels into two files.
Key fields should be the same of course.
eg.
Instead of loading fields: F1(key) F2(key) F3 F4 F5
I would load file with fields: F1(key) F2(key) F3 F4
Then I would load file with fields: F1(key) F2(key) F5
Just an idea 
Regards, Leszek
