Updating excel file with a master file

I have a master listing of customer accounts receivable detail in excel with many customer numbers. I also have individual excel files for each customer and am trying to update each of these customer files using a filter on the customer number for each file. I need to delete out the individual customer lines that do not appear in the master file (this indicates the line has been paid since the last update) and add in the new lines since the last update. I initially wanted to just apply a data table filter and copy/paste over all the detail in the customer file from the master file each time the bot is ran however in the customer file there is a column that is manually updated with comments based on communication with the customer that must remain in each row. If I copy/paste over the detail this is removed which is not what I want. The issue I have is I cannot figure out a way to remove the lines no longer included in the master file and add the new lines while making sure the existing comments for some lines remain. What would be a efficient way to perform both of these functions?