To keep it simple, I can migrate one site which has one single library. (I have many of these, built using the same template originally) the Structure migrates perfectly however the content of the library (pdf's, word docs etc) don't copy?! No errors in the logs. If I target the library directly it errors out complaining that the "list reference is broken".......
SharePoint on-premise list 'Documents' is skipped; Reason: The list reference is broken. The lookup field 'Document type' cannot find the referred list 'be335eb6-8d4e-4a18-8eeb-0830307e7f51', The lookup field 'Document status' cannot find the referred list '75c72f7e-d853-4d59-9f46-0293e20b9d41', The lookup field 'Discipline' cannot find the referred list '6ddda802-41ec-4bb6-b7d4-64bb8a617867', The lookup field 'Sender company' cannot find the referred list '10de1ad1-3b63-4b92-9ee7-ad04eb40c2aa', The lookup field 'Recipient correspondence in' cannot find the referred list '39c69c14-ac05-4578-84d2-504a750e6277', The lookup field 'Document type email' cannot find the referred list 'f918bf56-2f70-4dcb-b3d0-9b45dd77e7ad', The lookup field 'Document type corr in' cannot find the referred list '0db10bf3-ba7f-4136-adbe-420318687708', The lookup field 'Document type corr out' cannot find the referred list '2813d07a-fa69-490d-a364-80963229efd0', The lookup field 'Sender company corr out' cannot find the referred list 'fd46908a-6509-44ae-b4a5-2bf05b5937de' (ErrorCode: 0x02010023)