Thanks for bring up what appears to be a real problem for us.
I'm not sure if the clause you quoted extends to damage to the insureds boat or only to third parties damage, either way its a problem. I think the wisest course would be to write to the insurance company with your yards contract and ask a few "what if" questions. .46 cent stamp many save a lot of worry.
Lets assume the insurance says your boat and you are uncovered if damaged by the yard--and they very well say so because the insurance company has lost their right of subrogation against the yard, then you have a few choices.
1. Tell the yard their yard contract makes it impossible for you to get insurance that covers the boat--so how do they want to deal with it? Tell them they have to cover you by their insurance or
2. Get an exclusion from your insurance company or
3. change companies.
If this is a Boat/US insurance policy I think you could get some help from them.
thanks again

I recently suffered a lot of damage to my home due to super storm Sandy and the insurance companies are not so easy to deal with when it comes to pay outs so this is a topical subject, at least for me.

Notice I use the words "super storm" because if were a hurricane all insurance policies have a little known provision which limits reccover under the policy to 1 % of the values of the house no matter the extent of the damage. Do the math.