The Texas National Guard has sent letters to soldiers attending University of Texas campuses in Austin and Arlington, warning them that a conflict over military tuition assistance could cause them to lose thousands of dollars in aid.That could force the guardsmen to leave the colleges or pay tuition themselves, the letter warns."If no solution is reached, neither school will be eligible to receive Federal Tuition Assistance in the future," the Texas Army National Guard's Education Services Office says in the letter, which it sent Thursday. "This may influence your school choice if funding is an issue. ... Be cognizant that there is no guarantee that a solution will be reached and you may end up self funding your tuition assistance."Unlike the GI Bill, which provides money for veterans, the Defense Department's tuition assistance program is for active-duty service members. It pays up to $250 per semester hour, with an annual limit of $4,500.The conflict centers on how schools bill their students. The Defense Department says it will no longer approve the tuition assistance for schools that bundle their tuition into a single flat rate, as UT Austin and UT Arlington do.Instead, the Army wants universities to itemize fees so Army officials can approve tuition assistance course by course and ensure that federal money is not used on prohibited expenses, such as books and computers or application and graduation fees.UT Arlington switched to a flat tuition rate several years ago, spokeswoman Kristin Sullivan said. It made the move so students would know the exact cost instead of being surprised by added fees. For example, health and computer service fees are part of that flat rate. Books and computer hardware are not.The University of Texas System is negotiating with the Army, and the Guard's Education Services Office told students that it hopes to reach a compromise this month."We are going to work this out," Sullivan said. "UTA is committed in having transparency in its tuition rate."Thirty-one guardsmen are enrolled at UT Austin, according to the school, though not all receive the federal tuition assistance. According to the Texas National Guard, 46 students statewide are affected, including 24 in Austin.Information on guardsmen enrolled at UT Arlington was not immediately available Monday. UT Arlington's average tuition for 2012-13 is $9,292. Some majors, such has architecture and engineering, have additional fees for equipment.For Justin Scaffa, 29, a Texas National Guardsman since 2007 who is one semester away from graduating from UT Austin's School of Nursing, the dispute could have major ramifications. Scaffa said changing schools is not an option because nursing schools are not all the same. And he can't afford to lose thousands of dollars in assistance."I'm kind of up a creek without those funds," he said. "It's extremely frustrating. ... I wish they would come up with a solution instead of scaring the heck out of someone."Last year, the Defense Department started requiring schools to sign a memorandum of understanding before they can collect the tuition assistance from their military students.The memorandum was sparked by concerns that the military did not have adequate oversight over the nearly $600 million a year it was paying colleges -- particularly for-profit, online institutions.Staff writer Diane Smith contributed to this report.