on second thoughts (if you dont have loads of personal configurations and projects under jack) then simply
sudo apt-get purge jack*
will remove all jack and all dependencies and remove all user settings and conf files.
Then
sudo apt-get install qjackctl
to re-install
Dont perform the above...
If my understandings are correct the best tool is 'rsync'
it can do a one way or two way synchronisation between /folders/subfolders/files - also can do the -u (update only) for repeated scripted updates.
not sure which distro you are using but use your package manager (apt for debian and...
Have you interrogated the logs yet?
As you have Linux Mint (debian) then
sudo tail -f /var/log/syslog
will tail the respective syslog live - then when you try and start qjackctl look for 'qjackctl' entries with approx timestamps of the fails (start up errors)
CRTL+C to stop the tail.
Most live boot version of Linux are under 2GB when uncompressed - they are trimmed down versions of the DVD iso's.
As with any answer it needs to be known what you are trying to achieve?
If you want to play audio and edit movies etc - then try Ubuntu Studio ?
If you just want a solid desktop...