Ok so this is what I ended up doing. I moved the installation to another server using akeeba back up. Then deleted the account on the previous whm cpanel account, created a new account and restored the back up. So far so good. I think the issue is caused somewhere in how cpanel restores full back ups. We ran into a database issue on WordPress and that got me thinking if it was server related. I also disabled mod_security. Anyway right now everything seems fine I will update this post should that change.