Speaking from experience, the conduit should be capped and shown on a record drawing. There have been many times that I have gone back to a building (especially restaurants and hospitals) for a new project where I wish a conduit was still in place that had been demoed on a previous renovation.
IMO, if a conduit or raceway is in usable condition and is not in the way after being abandoned, it should be left.
I hate seeing a blanket requirement to "remove back to source" any unused conduit and wiring.
Roger