Kurt Mix is accused of deleting text messages about BP PLC's response to the disaster.
Defense lawyers said Thursday that the second of the two charges should be dismissed because it dealt with texts that amounted to inconsequential banter among colleagues.
U.S. District Judge Stanwood Duval agreed most of the texts were innocuous but said some dealt with the spill. He said a jury would have to decide their relevance.
Mix, of Katy, Texas, pleaded not guilty on May 3 to both counts. Each count is punishable by up to 20 years in prison and a $250,000 fine.