Collect all references creations (ReferenceChange which is an ADD as DifferenceKind, and whose ReferenceChange.getReference() is a containment) and put it in a list "createdObjects".

Browse comparison.getMatches() from the comparison from File1 to File2: (so LEFT=File2 and RIGHT=File1) : Do not change left match, but for right match, find a matching object.

If no matching object has been found, discard the match, its AllSubMatchs and its AllDifferences (actually stock them into a Set containing all the objects which will be deleted later:  "outDatedDiffs" and "outDatedMatchs".

If a matching object has been found, replace the right from the match with this matching object, and then browse the match Differences, and then browse the match SubMatches (same as we just did for the comparison matches).

Browse the Differences means: we need to change the ReferenceDiffs, Attribute Diffs will be merged naturally. For all ReferenceDiffs we browse, get the ReferenceChange.getValue() called "value". 
If value==null or if the current diff is a creation (ADD + isContainment), do nothing.
Else get the matching object for value.
    If the matchingObject!= null and if  matchingObject==value, it references a created object, belonging to "createdObjects"  list, do nothing.
    Else If matchingObject!= null, ReferenceChange.setValue(matchingObject).
    Else If the diff is a change required by a deletion on the right value (and we didn't find matching object as we are in the else block), we cannot discard this diff because the previous state will be corrupted by the deletion, so transform this diff as a deletion, so that the reference will be unset, prevents having an unresolved proxy).
    Else we didn't find a matching object, so we discard the diff, actually add it to "outDatedDiffs" set.

After that, we call EcoreUtil.delete on all elements in "outDatedDiffs" and "outDatedMatchs".

Finally, we create a BatchMerger from EMFCompare, and we copyAllLeftToRight the Diffs we want to.

End of the process.


What does find a matching object means:
if the source object is contained in "createdObjects" list, returns the source object itself.
else returns the matching object in the File3 resource, or null if there is no matching object.

How to determine if a Diff is a Change required by a deletion on its old value:
if diff is not a DifferenceKing.CHANGE return false;
else if  diff.getReference.isMany() returns false
else :
        if(diff.getMatch().getRight()==null) return false; 
        oldValue=diff.getMatch().getRight().eGet(diff.getReference())
        if oldValue != null : we return true if any of the  required Diff is 
                   DifferenceKind.DELETE 
                   and is a ReferenceChange instance 
                   and ( [oldValue is equal to requiredDiff.getValue()] or [matchingObject of value  is equal to requiredDiff.getValue()])
finally return false either in all other cases.