Editor: Loading cellrefs incorrectly transforms refNums, causing load failures

I've demonstrated this multiple times over other MRs and in discord discussions while working other issues. A simple explanation:

Perfectly normal refNums will often fail to load because CS has incorrectly marked the originating content file and thus cannot find the reference. One example can be seen simply by loading the Starwind ESM files:

but it gets even nastier than just this. When modifying references, which were modified by ANOTHER plugin, duplicates are created. The MOMW team attempted to make a patch for adanumuran reclaimed, which locks some doors added by Morrowind.esm. At present, the output of openCS does this to the references in our output plugin:

Record: CELL "punammu" Flags:0x0000 ()  
NAME: Name:Punammu  
DATA: (Interior) Fog_Density:1.00  Flags:0x0003 (Has_Water)  
NAM0: Reference_Count:2 
*FRMR: ObjIdx:411348  MastIdx:4  
NAME: Name:door_cavern_doors00  
FLTV: Lock_Level:2147483647  
DATA: X:-286.439  Y:-63.321  Z:-34.148  X_Angle:0.0000  Y_Angle:0.0000  Z_Angle:4.8124 
*FRMR: ObjIdx:94779  MastIdx:4  
NAME: Name:door_cavern_doors10  
FLTV: Lock_Level:2147483647  
TNAM: Trap_Spell:touchdrain block  DATA: X:-2148.165  Y:1985.416  Z:-30.825  X_Angle:0.0000  Y_Angle:0.0000  Z_Angle:4.782```

the mastIdx of the object is 4, even though this was actually defined by 1 (Morrowind.esm, not Adanumuran Reclaimed.esp`)