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Update: I disabled write permissions to the file a week ago and it has not been altered since. I haven’t seen any issues with website updates so I will keep it as is for now. I still don’t understand what was changing the file but this seems to stopped the problem. Thanks for the responses and help.

I tried changing permissions. I got a forbidden error. As far as Godaddy is concerned. Yes, they did help me with getting the site back up deleting the htaccess file. Something I had been doing anyway. They won’t help to find out why it’s happening. It has happened again this morning around 1am. Right now I am current with all WordPress updates.

Godaddy claims that WordPress is a third party software package and they don’t support it. The tech support wasn’t much helpful. I am disabling some plugins to see if there is a compatibility issues with the new versions.

I threw in the towel and just rebuilding it from scratch. Creating the WP site and installing the custom theme didn’t help.
Appreciate the help though. Now I will start another thread with a different question.