If you have uploaded invoices to the wrong folder (Sales invoices uploaded to the Purchases folder for example) or to the wrong company you can simply move these invoices from one company/folder to another.
In the inbox, select the invoice you wish to move by checking the box to the left (only a single invoice can be moved successfully at a time - attempting to move more than one at a time may result in errors):
Once you have selected the invoice you wish to move, click on 'Actions' and select 'Move' from the drop down menu:
A new window will pop up confirming the company name and folder you want to move the invoice to. The current company you are viewing will be populated in the Company dropdown, so you only need to change this if moving to a different company.
This feature is only available for invoices/bills. Moving invoices from Sales to Purchases or vice versa can cause some data to be lost, specifically line items or tax summaries depending on the invoice. These can simply be entered manually if this is the case.