Bizarre error with htaccess

Hi,
I am wondering whether anyone could shine a light on an issue I encountered across all the websites I manage. Earlier today all of the sites started responding with 404’s on all links within the sites. The front page was OK though. Just links.

Whilst I was investigating the issue I saw that the WordPress entry in htaccess was missing across all the sites. When I replaced this the permalinks began working again as you would expect.

Initially I thought a plugin was responsible but another site with the same plugin did not behave the same way. I use Installatron to manage updates and backups and the only other plugin with access to the htaccess file is iThemes security. We fell foul of the alpha pushout earlier on this month. Would that cause this behavior? I have written a cron jobbed script to check that these entries exist and if they don’t it appends it to the file.

Any help or suggestions would be most appreciated.