Magento – Upgrade to 1.9.2.2 – Base table or view already exists: 1050 Table ‘mage_permission_variable’ already exists

The issue is likely because you don't have a mapping of the resource name to the table name. Your getTable statement is attempting to access the table defined under hwcustomer/messages.

Ideally in your etc/config.xml file for your module you would have a config node that defines the entity:

<models>
    <hwcustomer>
        <class>YourCompany_Hwcustomer_Model</class>
        <resourceModel>hwcustomer_resource</resourceModel>
    </hwcustomer>
    <hwcustomer_resource>
        <class>YourCompany_Hwcustomer_Model_Entity</class>
        <entities>
            <messages>
                <table>hw_messages</table>
            </messages>

In this case hwcustomer/messages maps to the table hw_messages. In writing the SQL directly you likely helped avoid this issue because you're not using a resource locator to find the table name.

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