An excellent line! I like careful attitude to detail, it gives a sense of believability. I have long been interested in the Inca civilization and consider it to be one of the greatest worldwide.
Two points
1. Quipu is an excellent system for the collection and rapid transfer of statistical information. This is especially important in epidemics. The Incas would probably quickly learn to identify the symptoms of the disease, the incubation period, detect the most dangerous areas and dynamically introduce quarantines, opening or closing the corresponding roads. Even chaskis (messengers), in order not to become infected, could transfer quipu each other without coming into direct contact, but, for example, tying to a stone and throwing it at a distance. I believe that such steps, thanks to the high degree of obedience and organization of the population, would be extremely effective.
2. There are vague indications that some patterns, called tokapu, might be ideographic writing, in themselves or in combination with a quipu. The chroniclers have references to the fact that chronicles were recorded in Incan temples with help of patterns embroidered on the fabric.