The answer to this really depends on a couple of different things. First - what are you in the company? Are you a temp/entry level employee? Are you a 'supporting' position?
What do these things mean? Well if you are a temp or entry level position arguing about a particular duty, especially if it is a one off or rarely repeated duty and you are new, is the fast track to losing the respect of your supervisors. As a new, low-level or temp employee it is unlikely that you have the full context of the task. Perhaps there is a time line for moving to the paperless system that you are unaware of. Perhaps there is a reason(maybe even a legal reason depending on the data) that these documents need to be sorted. It's extremely likely that moving to a paperless system will be challenging and it is wise for management to take their time in deciding both the means and methods by which they intend to do so. Certainly ask about context and try to understand why the work needs to be done but, typically, work is assigned to be done because it, at some level and for some reason, needs to be done.
If you are in a 'support' position - it may just be that this is some unpleasant grunt work that's assigned your position. Sometimes that happens and yeah it's rarely fun or pleasant but every job has it. I was a chef for years and we purchased shell-on shrimp. 50+ pounds of it every week. Removing the veins and shells of 50+ lbs of shrimp is pretty unpleasant and we were looking for a purveyor that would sell high-quality, shelled shrimp at a reasonable price(ultimately we got both higher quality and better prices(even paying my salary) by purchasing shell on shrimp). What does this have to do with your situation? Shelling shrimp was unpleasant grunt work that had to be done in my kitchen. Sometimes, even as the chef, I had to be the one to do it. For every masterpiece meal I made there was a grunt task that was equally important and, honestly, that's pretty standard.
There's a saying about how being the best digger gets you a bigger shovel. And, yeah, that's true and you should be aware of it and working against it. But sometimes we all have to dig holes. And it would be a bit silly to complain about digging holes if you were hired as a hole digger right? Try to get some context about the task you have been assigned, try to understand the challenges both to moving to paperless and why end users make a mess of the data(that's a sign that there is a problem with how the data(hard copy or virtual) is arranged or presented as people tend to want to be tidy until there is a 'broken window'.) Then offer that understanding of the system and it's challenges to your supervisors.