Yes, although it will be a lot of fiddling or will have subtle issues.
removing an object: remove from MODF/MDDF, fix all MCRF in MCNK by removing the removed index and decreeing all bigger values by one. Alternative hack: set position to way below ground.
replacing an object: if path not present yet, add to MMDX/MWMO, add offset to MMID/MWID, replace id in MODF/MDDF entry. If model is bigger than before: add to MCRF of all spanned MCNK. If MODF, adjust extents size.
creating a hole: add bit in MCNK's hole mask.