Magento – Catalog Search reindex not completing

This is mostly due to any of the below two reasons

1. Server timed out and closed the connection.
   fix: try increasing the wait_timeout variable in your mysqld’s my.cnf/my.ini configuration file.
2. Server dropped an incorrect or too large packet.
   fix : increase the maximal packet size limit by increasing the value of max_allowed_packet in my.cnf/my.ini file.

You have already increased max_allowed_packet to 64 MB, try to increase it to 128 or more as well, if it doesn't work.
It seems to be resources issue only.
Also check if indexation is not breaking due to any other reason as well, just to make sure if indexation process is fine.

In my case I had two tables that were preventing a re-index. The first one was orphaned (https://stackoverflow.com/a/10622738/1055492): customer_grid_flat In /opt/bitnami/mysql/data/mydbname, I found only a customer_grid_flat.ibd file and no customer_grid_flat.frm file. I renamed the ibd file to ibd.old and this fixed the reindex for this table.

My second table design_config_grid_flat had both a .ibd and .frm file which I assume had become corrupted, to get this working I had to do four things (https://stackoverflow.com/a/18034693/1055492):

1. Rename both files
2. Copied the SQL that failed in the reindex and ran it it another temporary db
3. Copied the .idb and .frm file from /opt/bitnami/mysql/data/tmpdbname to /opt/bitnami/mysql/data/mydbname
4. Reindexed

Disclaimer

• The Magento 2 instance in my case is a Bitnami cloud virtual machine and your mysql location may vary.
• I take no responsibility for your lost data