So I know this used to be a common problem in M1.x. However, I only recently noticed this in our M2.1.3 environment.
How can I flush/wipe the Category flat data index and rebuild from scratch?
It normally happens when the memory limit is few, so increase on your .htaccess or NGINX config.
Run this command on your MySQL:
update indexer_state set status = 'invalid' where status != 'valid';
On you terminal run:
alias mage="php -d memory_limit=-1 -f bin/magento" mage indexer:reindex
You can also check mview_state table and set status to idle on that indexer then run it from cli with
php bin/magento indexer:reindex catalog_category_flat
If it break you should see some stack trace in the console