Thanks everyone for their input so far. (sorry for the delayed reply)
The markups we get back from site are lacking in most of the information needed to create a full accurate 3D model. Often missing vital information for our coordinated revit models, such as height or distances away from walls. And often late so its almost impossible to verify what has actually been installed as pipework or ductwork is covered by ceilings, floors or walls.
I know the fitters out on site have a busy time installing to a schedule, but in the BIM world we need to know what they have fitted, where etc (if they have deviated from the model) is very important when the contracts specify what accuracy our final models need to be.
I guess I was just hoping to copy/adapt some other company's workflow that works in a BIM world to ensure the models we produce and send to our clients are as accurate as can be expected.
I will have a look at the options mentioned above, thank you
