If you are upgrading from iBank 4 or Banktivity 5 to Banktivity 6, do not use Cloud Sync to pull down a fresh copy of your finances. Instead upgrade your existing iBank 4 or Banktivity 5 documents by going to:
File > New > Document from Previous Banktivity Version
This is important because transaction attachments do not sync and so they will be missing if you create a new Banktivity 6 document from Cloud Sync for the first time. Also, reports and account groups do not sync between Banktivity 5 and Banktivity 6.