Hey! Long story short: Yes, the Tang-era Uyghurs were still practicing Manichaeism when An Lushan revolted, but they are a separate people from the modern Islamic Uyghurs

The An Lushan Rebellion lasted from 755 to 763, and the Khagan of the Uyghur Empire had recently converted to Manichaeism, in 762. Other Uyghurs may have already begun practicing Manichaeism, since the Khagan's conversion occurred after meeting with some priests for 3 days. The religion continued to flourish in the empire and its people after its destruction by the Kirghiz Empire in 840, lasting until the Uyghurs submitted to Mongol rule in the early 1200 and possibly even longer

維吾爾 - modern Islamic Uyghurs

畏吾兒 - Tang-era Manichaeistic Uyghurs

The confusion regarding the Tang-era Uyghurs and the modern Uyghurs is quite common in English, since the same name is used for two very different groups. When I said earlier that they are separate people, I do not mean that they have absolutely nothing to do with each other. But as you can hopefully see above, their names are written differently in Chinese. The important thing is that you recognize that the words used to write Uyghur are different because the two Uyghurs existed centuries apart

The modern Islamic Uyghurs of today have only existed as a unified identity since around 1920. Before that, they primarily identified based on local oases and cities. They claim direct descent from the Uyghurs of the empire you mentioned, and that could indeed be true. However, the Mongol Empire had absorbed the Uyghurs in the early 1200s, and they mixed with Mongols, Han, Hui, and many other peoples along the Silk Road. As a result, the modern Islamic Uyghurs may be direct descendants of the Tang-era Manichaeistic Uyghurs, but the Tang-era Manichaeistic Uyghurs are not the only direct ancestors of the modern Islamic Uyghurs

EDIT: I made some changes so my answer would sound smoother and clearer

Sources

• Beckwith, Christopher I. Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present. Princeton, NJ: Princeton UP, 2009. Print.
• Lieu, Samuel N. C. Manichaeism in Central Asia and China. Leiden: Brill, 1998. Print.
• Thum, Rian Richard. The Sacred Routes of Uyghur History. Print.