The GP Partner Accounting on Computers ( identified, that eConnect does in fact truncate the GP Notes of a customer (and other master data) when updating records (UpdateIfExists=1), even, if you do not update the notes, they get truncated

Part of the reason, is that the variable used to handle the notes is limited to 8000 characters 

You are safe if you use TitaniumGP Copy/Paste function to update data, while it uses eConnect, it addresses and prevents this issue from happening.