If you can connect to the crm and get data from the selected view the upload should also work. (unless you have credential issues)
When you retrieve the view in the crm updater tool you'll notice that the lookup field needs to have the following format without quotes: "entityname","guid of the entity"
(so seperated with a comma)
When you try to export the excel file back to crm you'll notice the lines that have errors become red (or the fields) when you hover over the field with your mouse the error should become visible. What does that state ?
let me know if this helped.