Re-downloaded to make sure:
% grep GVA /Users/tim/Downloads/xplane_customdata_native_2408/navdata/Navaids.txt
GVA,GENEVA,115.750,1,1,195,46.253917,6.132222,1380,LS,0
GVA,GENEVA,115.750,1,1,195,46.253917,6.132222,1380,LS,0 <--- duplicate
IFFA,EGVA RW27 ILS/CAT I,111.100,0,0,195,51.682931,-1.817622,255,EG,0
IFFD,EGVA RW09 ILS/CAT I,111.100,0,0,195,51.684097,-1.762761,281,EG,0
SL,GVAC RW01 ILS/CAT I,109.900,0,0,195,16.753883,-22.949075,167,GV,0
SVR,SAGVAR,117.700,1,1,195,46.828056,18.117778,499,LH,0
SVR,SAGVAR,117.700,1,1,195,46.828056,18.117778,499,LH,0 <--- duplicate
%
Probably one line is derived from the VOR and the other the DME component, but given how the lines are exact duplicates the data is redundant.
Regards,
Tim