OK I stuck it out and waited for the empty dirs to sync, once it did so it deleted them all automatically just leaving the ones I wanted so while it wasn’t quite ideal, it did at least work despite looking like it was making a mess of things! Hopefully anyone else who comes across this will trust it a bit more as it did eventually work despite looking bad at the start. This was with the latest version available on the date of posting this (28th May 2016).