Thanks Jose,
I added a In-Transaction data directive and made a c# app to search for records with data in the UD field then edited the comment on the Invoice and called the Update method. The data directive takes care of the rest.
I noticed that after the data was edited I could no longer make valid edits to the comment field. Epicor says you can only edit payment holds, comments etc. I will do a test to see if teh cleaned data migrates to E10 and if I can then edit the comment field.
Cheers
Brett