Backups OF ALMOST ALL files is best done with the least amount of user apps running.
In use files can get 'locks' (to control multiple access),
Also, find some way to check your backups are
Really Being Completed as set up. ("I have the backups" , I look at the log and the last one
completed was 2 months ago

)
You don't (normally) need to backup apps that you can STILL download (eg Calibre), Jest the User data (Library And Settings folders).
The Backup issue that rears UGLY is when the source site goes dark or needs a fresh License Key to (re)activate. Hopefully, the creators of these programs has a continuity plan set up, just in case they get
hit by a bus.