If the following error is thrown while creating Smart Docs there are several steps to try
PDOException: SQLSTATE[08S01]: Communication link failure: 1153 Got a
packet bigger than 'max_allowed_packet' bytes: INSERT INTO
{batch} (bid, timestamp, token, batch) VALUES (:db_insert_placeholder_0,
:db_insert_placeholder_1...
Firstly you should update /etc/my.cnf by increasing max_allowed_packet to 100MB then restart mysql db.
If it still happens you should clear the cache with drush and truncate cache_update table.
A last option is to disable the update.module entirely.
If anyone has any other tips for resolving this issue please add to the comments.