$i=0;
$line2 = join '', grep { $i++ % 2 ? s/,/ /g : 1 } split /"/,$line;

##</code><code>##

1925,47365,2,650187016,1,1,
MADE FOR DRAWDOWNS, NEVER P/U
,16,IFC 8112NP,Standalone-6,,,44,10/22/2015,91607,,B24W02651,,
PA-3, PURE
,4/28/2015,1,0,,1,MAN,,CUST,,CUSTOM MATCH,0,TRUE,TRUE,O,C48A0D001EF449E3AB97F0B98C811B1B,POS.MISTINT.V0000.UP.Q,PROD_SMISA_BK,414D512050524F445F504F5331393235906F28561D2F0020,10/22/2015 9:29,10/22/2015 9:30

##</code><code>##

$i=0;
$line2 = join '', map{ $i++ % 2 &&  s/,/ /g; $_ } split /"/,$line;