I don't know about the effects of flocculation at this stage but I think it is not detrimental. The yeast got some time in glycerol and should be ready to be freezed no matter where it is located. In one study, cooling rate of 7°C/min (slow at lab, fast at homebrew conditions) was optimum for viability when cooling in absence of glycerol. Rapid thawing was very important, most likely to prevent reformation of crystals to larger units, although faster cooling rates could be fine with glycerol and adaptation time in cool glycerol may alter the results as well. It is a rather complex issue. Typical -15..20C is not optimum but can be used for some time. A tube too large may warm up at suboptimal rate when thawing and cooling rate and unwanted temp fluctuation(esp. freeze-thaw cycles of modern freezers) in smaller tubes can be controlled with insulation. So I encourage u to try smaller tubes and hints in say, this practical presentation:
https://www.google.fi/url?sa=t&sour...FjACegQIARAB&usg=AOvVaw0PTUEZhl5ShY6qewVhPTfN
And remember that after all, yeast can survive in a wide variety of conditions, unlike mammalian cells. So even if something goes slightly wrong, u are likely to see at least some viable (although stressed) cells that can be grown when starting on small volumes/on plate.