Probably the root cause is

Migration starting for database chromeos_autotest_db
Applying migration 058_drone_management up
Traceback (most recent call last):
  File "/usr/local/autotest/database/migrate.py", line 483, in <module>
    main()
  File "/usr/local/autotest/database/migrate.py", line 444, in main
    manager.do_sync_db(version)
  File "/usr/local/autotest/database/migrate.py", line 356, in do_sync_db
    self.migrate_to_version_or_latest(version)
  File "/usr/local/autotest/database/migrate.py", line 344, in migrate_to_version_or_latest
    self.migrate_to_latest()
  File "/usr/local/autotest/database/migrate.py", line 305, in migrate_to_latest
    self.migrate_to_version(latest_version)
  File "/usr/local/autotest/database/migrate.py", line 260, in migrate_to_version
    self.do_migration(migration, migrate_up)
  File "/usr/local/autotest/database/migrate.py", line 228, in do_migration
    migration.migrate_up(self)
  File "/usr/local/autotest/database/migrate.py", line 72, in migrate_up
    self._execute_migration(self._UP_ATTRIBUTES, manager)
  File "/usr/local/autotest/database/migrate.py", line 63, in _execute_migration
    manager.execute_script(sql)
  File "/usr/local/autotest/database/migrate.py", line 141, in execute_script
    self.execute(statement)
  File "/usr/local/autotest/database/migrate.py", line 128, in execute
    return self._database.execute(query, parameters)
  File "/usr/local/autotest/database/database_connection.py", line 304, in execute
    results = self._backend.execute(query, parameters)
  File "/usr/local/autotest/database/database_connection.py", line 54, in execute
    self._cursor.execute(query, parameters)
  File "/usr/lib64/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute
    self.errorhandler(self, exc, value)
  File "/usr/lib64/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler
    raise errorclass, errorvalue
_mysql_exceptions.OperationalError: (1050, "Table 'afe_drones' already exists")

Updating the migration version to 58 bypassed the issue but I am not sure of the root cause

 SELECT * FROM migrate_info, ()
    -> ;
ERROR 1064 (42000): You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near ')' at line 1
MariaDB [chromeos_autotest_db]> SELECT * FROM migrate_info;   
+---------+
| version |
+---------+
|      57 |
+---------+
1 row in set (0.00 sec)

MariaDB [chromeos_autotest_db]> update migrate_info set version=58;
Query OK, 1 row affected (0.01 sec)
Rows matched: 1  Changed: 1  Warnings: 0

MariaDB [chromeos_autotest_db]> SELECT * FROM migrate_info;
+---------+
| version |
+---------+
|      58 |
+---------+

I vaguely remember pprabhu bringing this up during our weekly team meeting.  Our migrations aren't actually consistent end to end.  

Can you post the affected builds?

Re #3: What I brought up in our meeting was only relevant for our TKO database instance. We dropped some tables manually in that instance of the DB at some point, so we can't apply migrations that modify those tables.

Shouldn't affect a brand new setup (as on moblab).

To me this just looks like too early a version to be migrated to. iirc, there is a db-dump at some point in the migration and we only apply migrations from that point onwards. I'm not sure what migration the dump is from, but 58 seems too old. 

I am cleaning my build out and re-syncing everything - I think somehow I got a bad build but not sure how getting a very old build would be possible.

I could not reproduce this - putting down to somehow getting a bad build.  Sorry for the noise.