The ~/Library folder is a real can of worms, mixing critical files that need to be synched (e.g. email) with others that should not be (e.g. hardware-specific licenses/parameters).Econ Technologies (ChronoSync) notes the problem ... The ChronoSync user manual has more details, including the suggestion of creating multiple smaller tasks that you then combine into a larger sync operation.
Meanwhile, here are some notes I found in Bombich Software's Carbon Copy Cloner documentation about all these kinds of issues: