I suspect that Ancestry uses a different lab for their autosomal tests. There is no indication that samples could ever be transferred. The Y-DNA samples are stored at Sorenson Genomics. It is not clear who did the mt-DNA testing. FTDNA, to their credit, is the only firm that foresaw this problem.
However, Y-DNA project managers were in a Catch-22 situation. FTDNA used Arizona Research Laboratories for their standard Y-DNA panels. Some were a bit skeptical about the quality of their results. From what I can tell, FTDNA now does all of their tests in-house and the quality is excellent.