If it makes you feel any better, I had mine in milk jugs, plastic bakery containers, etc. and we got very heavy rains at least twice - maybe three times - and they were really flooded as well. I think almost all of them germinated. Each time, I removed the lids on a few sunny afternoons and let them dry out as much as I could and then replaced the lids at night. It was a bit of trouble, but they were really soaked. I thought about more drainage holes but didn't do that because I kept thinking, if I do that it will stop raining and I'll be watering them a lot.
Maybe someone else can share their experience with flooded containers, but most of mine seemed to turn out okay. Hope that is the case for you, too!

I've had the same problem. I had to take mine out of the containers today to help them drain some. I did find some of those plastic milk crate box things to hold my 2 liter bottles. They have helped keep them together and the critters from disturbing them. They didn't get water logged like the others in regular containers. I will just place the whole thing into the larger containers when they need to be watered. It is much easier bottom watering 200 containers that trying to gently water each one.

You seeds should do fine. You can always create a few more containers of the ones you are really concerned about, but still keep the ones you have already. You may just end up with extra to share.

Pam

If you got around to draining off the excess soon enough it might even help. Note on several forums like Growing from Seed it is sometimes suggested to soak some seed before planting. A Google search on soaking seed and gardenweb gave me about 33 ghits and soak seed gardenweb gives me over on hundred.