I need to populate user profile properties from a flat file as the properties do not exist in AD. These fields include title and department, among others. Azure AD Connect has not yet been installed in this environment. My question is that if I disable syncing for certain attributes in Azure AD Connect, will those fields be overwritten by the 'AD Import' process in the Office 365 user synchronization pipeline?
The AD Import process will synchronize regardless if the properties are populated or not. This means that yes, your populated values will be overwritten by blank values.