Mackup creates the backup folder in the Box Sync local folder properly and all dot files (.bash_profile, .bashrc, .gitconfig, etc.) are copied there but they are never synced to Box, which means that after the local Box Sync folder is deleted, the dot files will not be restored from Box.

This is due to Box Sync ignoring files that start with a dot "." as hidden files.

Documented here: https://community.box.com/t5/Box-Sync/Which-File-Types-Are-Ignored-Or-Blocked-In-Box-Sync/ta-p/117

The way around this could involve copying the files to names that do not start with a dot and creating symlinks back to the original dot file names, e.g., .bashrc -> Box Sync/Mackup/bashrc.txt