I have a large macro enabled workbook that processes data and exports it in a usable format. Some of the data that it processes can be large and take a while to run through the workbook. I'd like to be able to open this workbook multiple times to process multiple data sets at once. Is there any way that this can be done? 
I am using a python 3 app that I developed to manage the books and am more than open to using other languages and software.
Think about your problem here.
Assuming the workbook that processes the data is essentially a model, with input and output, what you could simply do is make copies of that workbook ahead of i/o model run.
So you've gout 1-10,000 rows of data for Model1.xlsm 10,001-20,000 rows of data for Model2.xlsm.
Obviously this is hackneyed, but the fact that you have to do this with Excel and not just use python for calculation means this is probably the easiest way to overcome the problem.
Any way to run multiple instances of the same excel workbook with macros?