We are certainly only discussing pure depth maps.
I would definitely always save the originals on hard drives, if possible on two separate ones.
For use in RM, however, I would export all data from a very large project as a csv, because then changes after editing are also included. I use this csv as a template to add new data and save everything again as a csv. The next, new RM project with the newer csv data will then certainly perform better.
In order not to keep adding new log data to the same data, I use GIS programs (and the aforementioned csv in them). By buffering the existing points and comparing this geometry with the new points, I can specifically select only the newer points and add them later.
For large amounts of raw data, for example when exchanging data with other users, I also use the IMC's sonar mode if the other users do not have RM.