This part doesn't make a lot of sense to me
"as i actually want to be able to edit word and excel files on my pda

not just edit them...."
If what you wanted to say is not just view them, then it's nothing to do with your file conversion. You just need to get your file associations right again. You'll have to edit the registry using a registry editor. Go to HKEY_CLASSES_ROOT and delete .xls and .doc . The next time you start a doc document or excel document from File Explorer, it'll ask you what program you would like to use to run the file. Just choose Word Mobile or Excel Mobile and select the box that says something like use this to run in the future.
Hope it works.