Well really any new customer records, Sales Orders/Opportunities, Contacts, and Ship To Addresses are all potential items that may need to have the links re-established. So I would document those.
The CU file structure will be in sync, but the information contained within them may have discrepancies. My assumption in the response above was that you would be creating a test environment running in parallel to a live environment. As such, if you upgrade the test environment, it's not capture the addition of records to the CU tables that have been made in the live environment. Hence the necessity to run the Rebuild CRM utility to ensure that the mirrored tables are populated with the most up to date information and all records that may have been created in one system or the other and synchronized are linked and synced correctly.
My concern isn't more based around the file structure itself, but rather the integrity of the synchronization itself as that is the biggest hassle of the native Sage integration between 100 and CRM.