Hi Martin,
I came to know very recently that deski reports can be migrated to 4.1 and then converted which is would give better results. Unfortunately I have not been successfull in finding the thread but I believe it was Sebastian Wiefett
who had updated me with the same.
Else you may refer the document
BI 4 How To: Planning the Desktop Intelligence conversion to Web Intelligence
if you would like to convert the Deski to webi in 3.1 and then upgrade to 4.1
Good luck with the upgrade