I still can't imagine why an outdated developer should remove the emulsion in flakes. This simply does not make any sense.
Try to see it the other way: The developer contains flakes (wherever they might come from). The flakes stick to the emulsion during development, leaving the underlying area undeveloped. Some of them come off at later steps, producing the impression of "holes" in the emulsion (which are in fact just undeveloped areas).
Ordinary brown glass bottles are (in my experience) not suitable for sorage of C-41 developer (as well as other highly alkaline developers). Use borosilicate glass instead, or PETE plastic bottles (although HD-PE may be okay for a few weeks).