You shouldnt even have to save the workbook that runs the code since that is all the extra workbook is for.
As for the double commas deal yes that can easily be added (I may be able to have it done later tonight)
As for the column D not getting fixed that is strange. You mentioned a 2nd folder? are you running the code for just one folder? it will only change documents ending in .xls or .xlsm that may be the problem because I believe .xlsx is a valid extension. I will change that. are there any other file types it may have skipped.

I will try to get the corrected code to you soon.