Gee, sorry this has take so long...
Actually, I don't know what effect vacuum sealing might have on lily seeds, if any, but it is certainly not a natural phenomenon, so it could have adverse effects. I've never heard of any of the Lilium hybridizers doing that.
There is no need to seal in moisture with lily seeds, which is the whole point of vacuum sealing food. In fact, moisture can lessen the long term life of lily seeds. My gut feeling is that vacuum sealing lily seed is a bad idea.
If you have done it already and they are in the freezer, and the freezer does not go through automatic de icing cycles, I think I would leave them be. But, open the seal as soon as you remove them. If ice crystals have formed inside the vacuum seal, even if you can't see them, they can moisten the seed when thawed, and damage the seed by initiating germination before you want it. It's really surprising how little moisture some lily seeds need to begin germination.
If your freezer has auto defrost, then I would take them out and repackage them, and read this thread:
