Upon further investigation there seems to be a problem with the ALTER command. This is the error I get when the table is not readable anymore:
| 123456 | dbName | localhost | userName | Query | 12345 | Waiting for table metadata lock | ALTER TABLE wp_wc_category_lookup CHANGE COLUMN category_tree_id category_tree_id BIGINT UNSIGNE | 0.000 |
This error happens everything our hosting provider tries to do a database dump, it will repeat until in the morning the multiplied processes are all killed.
Any idea why the database dump would do that to the system?