I've experienced this issue of late. My work process is to import the scan files, register them and then create regions. Typically I isolate the building(s), the wider context and finally the topography - which I then load into Cloud Compare to reduce the number of points, export the reduced file as a txt file and then create topography in Revit using the 'from imported file' option.
The issue arises when I try to import point clouds (as separate regions) into revit - the point clouds don't align and the topo created from the txt file can be way out....
The solution I have found is to create the regions in Recap in the normal way (building, context, topography etc.) but instead of importing them into Revit as separate files import the whole Recap file instead. In Revit you can then use VG to select which regions you want displayed.
Hope this helps.
Darv