hello, my name is Asaf Algawi, I'm a software engineer with more than 4 years of experience in .net development.
I have several solutions to your problem
1. if you have the source code for your software the easiest solution was to add a feature which uploads the documents.
2. if you don't, the next best thing would be to monitor the folder holding all patients documents periodically, say everyday after closing time, or when the computer starts, or any other time depending on your work habits, then upload all newly created or edited documents automatically. this can be easily achieved with some windows service without actually interfering with your program or its code.
these are the simplest and best solutions in my opinion.
if you choose my services, I would develop the software as a .net application, with a simple ui used for configurations (where to upload, what time, etc...)
hope you select one of them and my services to implement them.
waiting to hear back from you,
Asaf.