This just screwed up with my settings. I was lucky that I had almost everything backed up.

The problem was with Mackup, in the sense, for it to 'backup' (which I assumed would just copy/paste the files) had actually moved the contents to Dropbox and created the symlinks in place. Therefore not a true backup!! :(

I guess what I am trying to say is that please be VERY SURE of what the 3rd party tool/script does before you use it, cause sometimes you might just 'rm -rf' the seemingly useless artefacts.

Screwing up your work environment is NEVER fun!