Thanks I'll give it a try. But I do have auto updates disabled and it still happens. I installed the non root version and have not had this issue since.YouTube Vanced is being overwritten by stock YouTube because they have the same package names (which is the very benefit of Vanced root) and PlayStore sees an update available so installs it, thus over writing Vanced with Stock.
Simple fix : Install TeMeFi and detach YouTube from the PlayStore.
Personally, I've also disabled auto-update apps on the PlayStore and just manually update every couple of days. Not sure this is entirely needed as YouTube never shows up on available update lists, nor do I get any notifications that an update is available, however it's just easier for me this way.