I found something interesting as I was reading True Crimes in Eighteenth-Century China by Robert E. Hegel. While describing the judicial system for capital crimes, this fact came up, but Hegel doesn't explain why. What was the incentive for the Qianlong emperor to issue a blanket pardon, and so many times?
I'm not an expert on Qing law, but I'll try to answer this as best as I can with limited resources.
According Klaus Muhlhahn's "Criminal Justice in China" (page 50), Qianlong warned that "confessions obtained by jiagun and cudgel are not necessarily entirely reliable." This posed a problem for Qing officials, as under Qing law, "until the offender confessed, the magistrate was unable to pronounce a sentence. Since there were strict time limits for each case that the magistrate had to comply with or face administrative penalties, the use of coercion was a practical necessity in all cases in which the offender was not willing to confess and refused to admit guilt." (Page 49)
In Hegel's book, he notes that reduction of punishment was used "in the name of the (paternalistically merciful) emperor, thus demonstrating his leniency towards fallible commoners." (Page 13). Hegel also states that there was a shortage of trained judges, as the education system was designed to produce scholar-officials, not judicial figures. As there was a six month (page 14) limit on how long a case could be conducted, no doubt torture was commonplace, to the point that Qianlong had to call attention to and minimize its usage.
Qianlong had made many efforts to ingratiate himself with the local population. Jonathan Spence commonly writes how Qianlong portrayed himself as a classical Confucian emperor. This was partially motivated by Qianlong's understanding how innately tenuous Manchurian rule could become, given the far larger Han Chinese population. My guess would be that Qianlong's eleven general amnesties were given to promote the image of a merciful emperor. He could not afford to allow his officials to engage in excessive torture for fear of undermining the Qing Dynasty's position. However, if a confession could not be extracted, a sentence could not be passed. In these instances, Qianlong likely chose to demonstrate his "benevolence" as an enlightened ruler by letting the accused go, rather than allow the state to be seen as ineffective by not being able to legally and successfully prosecute the accused. An amnesty simply absolves one, but does not indicate guilt or innocence. In the end, the accused gets a warning, Qianlong is seen as benevolent (and possibly possessing some secret knowledge), and the reputation of the state apparatus is maintained.