This probly ranks among the sort-of-supported, but it's not any SQL hacks involved so I think it's sort of kosher.
All info is taken from https://community.dynamics.com/crm/f/117/t/140108 which in turn points to a bllog. This is a summary of that.
First, run the following SQL command on your organisation db:
That will give you a guid to a mapping page which is interesting. When you want to do the same thing on quote to order mapping, change the target to "salesorderdetail" and the source to "quotedetail"
Now we use the guid provided by the nice database in the following URL: http://[x]/Tools/SystemCustomization/Relationships/Mappings/mappingList.aspx?mappingId=[y]. Change [x] to serverurl and organisation (myserver/testorg/) and the [y] to the guid just found in the database
This opens a mapping page where you can insert mapping from sequencenumber to sequencenumber and the products will be in the same order in both records.
I'm pretty much posting this to make it easier for me to find, maybe it's good for someone else too. Again, I haven't found out how you did this, just to make sure.
Developer at CRM-Konsulterna