As part of serialization, the code which collects the set of indexed FSs has a portion which removes duplicates; this is run on an IntVector object which is collecting indexed FSs for a single type, FSIndexRepositoryImpl line 1531). This object is cleared and reused, in FSIndexRepositoryImpl, lines 1522 to 1532..
There's an edge case bug where this dedup routine fails for empty arrays - it returns an array of length 1, where the value is whatever might have previously been there before the last "removeAllElements" (FSIndexRepositoryImpl, line 1522).
If the 0-th element in this working IntVector happened to be 0 (which is the case on first use), then this will include the FS at address 0 (which is null, and has a 0 type code, etc.), which causes XmiSerialization to fail.
The only time this error would manifest itself as a NPE is if a used, but now 0-length index for some type was the first index to be iterated over.
Peter Klügl found this via a NPE while serializing a CAS, and it was order dependent. I reproduced it by making a CAS, adding / removing an instance of an annotation (which is a sorted type), and then setting the text for the CAS (normal operation, setting the text for the CAS, then doing the other, would result in the DocumentAnnotation instance being created as part of setting the text, and it would be found 1st in the index collection code, thus insuring that position 0 in the working IntVector was not 0).
The fix is to handle the edge case where the input array to sortDedup is of 0 length.