Some studies have reported some loss of viable cells, but I'm not aware of any studies reporting major loss or damage, to the point where it would completely eliminate the advantages of freezing.
There are tests being developed based on changes in the red cell membranes, but as 13 notes, you can't just spring them on the peloton. The phthalate test that caught Contador by surprise is a good example. Though in the end it was allowed as supplementary evidence, it was not allowed to be used as a standalone test.
The case of CERA is somewhat different, since it was just a modification of previous tests for EPO. It had already been established that any test demonstrating the presence of synthetic EPO was valid evidence of doping, so as far as approval goes, the heavy lifting had already been accomplished. This was not case with the phthalate test, nor would it be the case with the current research on degradation of red cell membrane markers. Approval of such a test would require evidence that these changes are significant in transfused cells, and they don't occur in endogenous cell populations.
I'm not sure what you mean by 'the added issue of the sudden increase in old cells". The fact that the cells are "old" is only relevant if there is a test for old cells, which as just discussed, does not yet exist in approved form. Transfusion of course does result in an increase in mature cells, but this is masked by dilution, and its suppression of retic formation, as always, is masked by using EPO to stimulate the latter.
At the risk of being ridiculed, I will bring up the possibility of beetroot juice. IIRC, Horner was claiming he used that before? There are some studies of its effects which suggest that while on average those effects are not very great, in certain individuals (super-responders?) there might be a large benefit.