Editing a chunked terrain with a noch chunked representation terrain (RT) is possible.

You take a bitmap, that serve for the complete heightmap, if it is too big you store a image list of chunked bitmap parts, but if a integer ratio (4 chunk bitmaps store each 2x2 cells of the chunked terrain). So, you could move the RT to the current cell of the chunked terrain (determine it by checking againste the camera center vector), when the RT swaps to another cell, save the heightmap data into the appropriate bitmap or bitmap chunk or subchunk (if one chunk represents more than one terrain chunk). During swapping and saving you can deform the mesh with the heightmap data of the tied bitmap/-chunk/-subchunk and then do the whole editing process with RT for that part of the terrain. To save the terrain file I suggest you have to write it manually to the disk, I'm not familiar with chunked terrain.

A new suggestion by me: please let the user select faces of polygons of a model and then delete the selected faces, also for the model. If you edit one model, duplicate the real file and add a suffix at the end - to prevent that all models became changed and the source model is unchanged (perhaps you can let the user decide this by an option task to do this nevertheless). Add also selection options like select inverse or so constrainted only on that one model.

Thanks.