If you're looking to utilize Eikon data in R, I would suggest retrieving it straight into R using Eikon Data APIs library for R without Excel as an intermediary.
If you must use Excel files, then in a generic use case you need to add VBA code to your spreadsheets that ensures that Eikon Excel COM add-in is loaded into Excel session and is signed in. Attached is an example of a spreadsheet with a sample of this VBA code and Visual Basic Script that creates a new instance of Excel application, opens this spreadsheet, synchronously refreshes Eikon formulas in it and saves and closes the spreadsheet. You should be able to easily replicate this Visual Basic Script sample in R.
UpdateEikonSpreadsheet.zip
