This Daily Kos article suggests that if Indiana State Courts rule that November 2010 votes for Charlie White are deemed not to have been cast (on the theory that the Republican nominee for Secretary of State, Charlie White, wasn’t eligible to be on the ballot), then the Republican Party would lose qualified status and would need to submit petitions for all its nominees in 2012 and 2014.
UPDATE: however, the Daily Kos author seems unaware that in 2011, the Indiana legislature passed HB 1242, which says that when a state recount commission makes a final determination that a candidate for Secretary of State is not eligible, that determination does not affect the validity of the votes cast. Thanks to Rick Hasen for the link.