Hi Dan,
Yes they were there. I have hundreds of .mxds and often need to apply transformations. Recently between WGS84 and Arc1950. Looking back over the last week's work I realised that in cleaning up my machine I had uninstalled ArcEarth and Arc App Studio. Presumably the uninstall from one (or both) of those two was a little overzealous and took all the transformations with them.
In order to fix it it was as simple as Control Panel > Programs and Features > ArcGIS 10.4 > remove / change > repair
Now they're all back.
Success.