Likelihood of truth
We're talking about one or two bagua bodyguards, and then three baji bodyguards, out of how many--dozens? thousands?--of royal bodyguards during that time. Your sources suggest that the bagua-to-baji idea is at best an oversimplification and probably just a saying unless you find more substantial evidence.
That said, it is an interesting question.
What do we know about the bodyguard business in late Imperial China?
Kennedy and Guo, in the excellent Chinese Martial Arts Training Manuals: A Historical Survey, note that bodyguarding was a common way for martial artists to make money. It would be hard to say that they were primarily bagua-, baji-, or whatever else practitioners:
By the mid 1800s, the favored secret weapon of bodyguards was a Colt pistol... The popular image of a Qing dynasty bodyguard is a skilled swordsman using his saber [or bagua -Dave] to drive off bandits. In reality, he was an intelligent man using his reputation, his connections, and his diplomatic skills to protect his charge, all backed up by a gun.
That being said, these guys did know hand-to-hand combat:
The general public associated the martial art of San Wang Pao Chui, The Three Kings Cannon Pounding style, with the Qing-era private security business... Non-Shaolin systems were equally well represented, however--in fact if not in public perception. The internal systems of Xingyi and Bagua were also common systems of choice for men working in private security. It is important to keep in mind that the majority of private security guards spent their martial arts training time with weapons work, just as it was in the military.
However, this was the private security business. Also, I still haven't tracked down the (possibly nonexistent or apocryphal) source of your claim, to wit, that bajiquan has acquired a reputation as the Emperor's bodyguards' martial art of choice.
Bagua and Baji Bodyguards
As for bagua being the style of earlier bodyguards, there seems to be some evidence that some bodyguards did bagua, but what does that tell us? Passages like this shouldn't be ringing your Interesting Martial Arts History bell, they should be setting off your Chinese Martial Arts Marketing alarm:
Under Grandmaster Chu, Gong Zhong Xiang learned Xingyiquan, Xingyi Bagua, Taiji Splashing Hands, Stationary and Dynamic Push Hands, and both long and short range weapons. Gong was Chu's most devoted and talented student. Chu placed complete trust and confidence in Gong, passing on to him secrets that he imparted on no other student. Master Gong also studied under the King of Chinese Pugilism, Wang Zhang Fei, a student for over 15 years of the legendary Imperial Baguaquan master Gong Bao Tien - a personal bodyguard of the Emperor during the last years of the Qing Dynasty. This Imperial style Bagua was taught exclusively to the Imperial guards. It's superior fighting techniques were a closely guarded secret, never being taught to the public to ensure the safety of the emperor.
Yin Fu [of Yin style Bagua] later became the personal bodyguard of Emperor Guang Xu and Empress Dowager, the highest prestige position of its kind in the entire country. Royal merchants along with the imperial court depended on Yin Fu’s Bodyguard Company for protection. Yin Fu taught the complete baguazhang system to Men Baozhen who taught Xie Peiqi, who taught He Jinbao the current grand lineage carrier.
Closely guarded secrets. A special style. The complete system, only available through our school. Taught exclusively. No other student. Secrets. "Xingyi Bagua". This is hyperbole, not history. Were there bodyguards, perhaps instructors even, who studied bagua? Of course. Was it the official style? Was it the most common? Was it even a big deal what hand-to-hand martial art they practiced, considering weapons were so much more important? No.
This claim about bajiquan being the Emperor's bodyguards' style is repeated nearly verbatim to the Wikipedia version across the internet. Let's suppose it's true. Was bagua or any other style dominant among the Emperor's bodyguards? Do we really think that the modern Chinese version of the secret service would care enough about hand-to-hand combat, or attachment to any style, to pick one single or primary style of kung fu to teach? I see no credible reason to say so yet. So the assertion "Chinese leaders' bodyguards used to study baguazhang, and now study bajiquan" is groundless on both the first and second clause at present.