Just had this happen to me today. I think I found the solution:
Using this as a reference point: Upgrading ERPNext Version 6-9
frappe@ERP:~/frappe-bench$ bench mysql
Welcome to the MariaDB monitor. Commands end with ; or \g.
Your MariaDB connection id is 177
Server version: 10.1.25-MariaDB-1~xenial mariadb.org binary distribution
Copyright (c) 2000, 2017, Oracle, MariaDB Corporation Ab and others.
Type ‘help;’ or ‘\h’ for help. Type ‘\c’ to clear the current input statement.
MariaDB [1bd3e0294da19198]> ALTER TABLE tabFees ADD COLUMN grand_total DOUBLE(9,2);
Query OK, 0 rows affected (0.26 sec)
Records: 0 Duplicates: 0 Warnings: 0
MariaDB [1bd3e0294da19198]> \q
Bye
frappe@ERP:~/frappe-bench$ bench update
INFO:bench.utils:updating bench
INFO:bench.utils:git pull
Already up-to-date.
[…]
INFO:bench.utils:sudo supervisorctl restart frappe-bench-workers: frappe-bench-web:
frappe-bench-workers:frappe-bench-frappe-schedule: stopped
frappe-bench-workers:frappe-bench-frappe-default-worker-0: stopped
frappe-bench-workers:frappe-bench-frappe-long-worker-0: stopped
frappe-bench-workers:frappe-bench-frappe-short-worker-0: stopped
frappe-bench-web:frappe-bench-node-socketio: stopped
frappe-bench-web:frappe-bench-frappe-web: stopped
frappe-bench-workers:frappe-bench-frappe-schedule: started
frappe-bench-workers:frappe-bench-frappe-default-worker-0: started
frappe-bench-workers:frappe-bench-frappe-long-worker-0: started
frappe-bench-workers:frappe-bench-frappe-short-worker-0: started
frappe-bench-web:frappe-bench-frappe-web: started
frappe-bench-web:frappe-bench-node-socketio: started
Hope this helps!