My understanding, and from what Ashenden and others have written, is that if the samples are frozen and stored properly, there is no issue with their integrity. Attacking the Lab's records as to storage temps, service of the freezer, etc etc will be hammered but I cannot imagine the US Feds would undertake this action unless they'd already nailed down the veracity of what they were obtaining.
The "purported" issue with the 99 TdF samples before was that they were research study samples and there was not the full Chain of Custody documentation that would exist if they'd been used for an anti-doping test. The A's had been declared "clean" which is another factor they tried to lean on in the Vrijman document
Now, if these samples have been stored properly, and were not part of a research study where their CoC will be subject to dispute and attack, the urine should not have any problem being thawed and be suitable for testing. Bearing in mind that EPO can degrade, not magically appear, and that the newest forms of the tests for EPO, CIR and DEHP most likely will be applied if there is enough urine.
The issue of how to get the all sample numbers which are Lance's is solvable. Ressiot already had some of the numbers, and the UCI still has the numbers. I don't imagine it will be hard to obtain Lance's sample numbers by his own suggestion, as he claimed he'd cooperate. Recent development, like McQuaid's turnaround comments, and Lance's sudden withdrawal from the sport again, now make a little more sense.
Urine can, and probably will, be DNA tested to determine if they are from the individual. Funny thing, recall the notion that no one noticed Lance's cancer despite him being tested? Begs the question of they were looking at his urine at all during that time, huh?
I predict his samples will glow like spent nuclear reactor rods when run through the CIR process, and very well could have big spike for DEHP once EPO went out of style.
Let's keep in mind that proving the guy used PEDS in criminal court is different than proving it in anti-doping arbitration. Burden of proof is higher but they are not confined by the strictest of testing methodologies. A DEHP test already exists. It might not have yet been validated for WADA but the medical and forensic lab community has a myriad of tests that they use everyday that are not part of the anti-doping world. Fighting evidence of DEHP spikes from having a DEHP test run by an FBI lab or a highly reputable medical facility will be hard to undercut.