Another major merger transition for American Airlines (AAL) - Get Report is scheduled for this weekend, as the carrier plans to integrate its three pilot-oriented flight operating systems into one.

American hopes to replicate the smooth transition that accompanied its cutover to a single reservations system a year ago, although it is sparring with the restive Allied Pilots Association over the union's involvement in the flight system integration. The conflict isn't expected to impact the weekend transition, however.

The flight operating systems involve about 500 software applications that manage crew scheduling, aircraft dispatch and movement and other functions. American still has separate systems for America West and US Airways, which merged in 2005, and for American, which merged with US Airways in 2013. The three legacy airlines employ a combined 15,000 pilots.

FOS "creates a single pilot workforce," said Kimball Stone, vice president of flight, on a conference call with reporters on Friday. Pilots "can fly any aircraft throughout the system."

Among the changes, pilots will be able to bid for trips under the new integrated seniority list that was announced this month. Although some former America West pilots see flaws in the new list, Phoenix-based former America West pilots will be able to bid for flights outside of Phoenix for the first time since the 2005 merger.

The first joint contract vacancy bid is set for Oct. 19, Stone said.

The transition to the single FOS is scheduled to begin late Friday, Sept. 30, and to continue into Saturday, Oct. 1.

During the weekend of Oct. 17, 2015, American successfully completed the cutover of its reservations system. The transition was closely watched due to problems with previous post-merger reservations cutovers, particularly the one that followed the 2005 merger of American and America West, and because it involved systems that interfaced directly with passengers.

Afterward, American promoted Maya Leibman to executive vice president, as CEO Doug Parker declared, "Maya recently led a team that completed the most successful reservation system cutover in aviation history as evidenced by widespread employee readiness and zero customer disruption."

On Friday, Leibman, now overseeing the FOS cutover, said, "We are every bit as alert and focused. {We are} investing as much time and energy as we did" for the reservations cutover." She said that more than 60% of the preparation will be done before Oct. 1 and that 150 years of training -- equivalent to 150 employees training for one year -- has occurred.

The transition, like the 2015 reservations cutover, takes place at a time of reduced demand for flights following peak summer travel and preceding holiday travel periods.

American's pilots said they were cut out of the planning process.

"Flipping the switch to integrate three separate flight operating systems in a single day poses a significant challenge for our airline," said APA spokesman Dennis Tajer. "APA offered to help in the transition to a single flight operating system. Unfortunately, management did not take us up on our offer of a mutually beneficial partnership.

"For the sake of our pilots and other front-line employees and most importantly our passengers, we hope the transition goes smoothly," Tajer said. "To that end, APA will operate a phone bank of pilot volunteers to assist pilots flying the line as the airline merges three complex computer systems into one."

Stone acknowledged that the airline and APA "have outstanding issues" but said next week's cutover does not involve flight operations, but rather systems that support how you bid for vacancies, scheduling, vacation management, timeline for which we pay you, largely administrative, quality of life kinds of things." He said no safety issues are involved.

American will still have work following the Oct. 1 transition. The airline still has to design a system to merge contracts for flight attendants from American and US Airways. The task is taking more time than expected, apparently because existing software cannot manage the complexities.

"We're working on a plan for that, coming up with the best date for that," Leibman said. "We're absolutely committed to getting this right."

This article is commentary by an independent contributor. At the time of publication, the author held no positions in the stocks mentioned.