Okay, I'm slowly getting there. It seems like updating SystemEditor in 
MC in 3.10 somehow broke it - some methods were simply referring to the 
wrong ivars which caused SE not to work at all. Recompiling the SE 
packages fixed that.

Secondly, the issue I was seeing with the iVars being incorrect are one 
of the subtleties that SE currently doesn't correctly deal with. Here is 
an illustration:

testCleanupOfOldInstances
   "Ensure that old instance are cleaned up properly"
   instance := CleanupTestClass new.
   Smalltalk garbageCollect. "for easier results make it old"

   self assert: CleanupTestClass instanceCount = 1.

   ed := SystemEditor new.
   (ed at: #CleanupTestClass) addInstVarName: #whatever.
   ed commit.

   self assert: CleanupTestClass instanceCount = 1.

   ed := SystemEditor new.
   (ed at: #CleanupTestClass) removeInstVarName: #whatever.
   ed commit.

   self assert: CleanupTestClass instanceCount = 1.

The problem is that since #become: changes class pointers you *must* 
clean out the old instances or otherwise they'll be completely and 
utterly broken when you finally #become: the classes itself. This can be 
achieved by placing a strategic full GC in the right place in the 
migration process (I'm not sure where that would be in SE but probably 
somewhere in the migration transaction).

Cheers,
   - Andreas