Updating Excel Data Sources - Best Practices

Due to constraints outside of my control, I am unable to establish direct connections to the systems/data sources of much of my work. To get this data into Power BI, I rely on exporting to Excel and utilizing that source. I often have to update these files based on newly exported data. Normally, I will save the new file over the old file or copy and paste the contents of the new export onto the old file. This method of updating usually works, but sometimes I encounter errors. Some I can find the root cause and others I can not. I realize that this is not the ideal approach but its best I can currently do. What best practices are out there for updating Excel data sources? Is there an entirely different approach that I am unaware of?