I had my 5 acre lake fertilized a couple of weeks ago.
We had a storm dump 8" of rain in one night which turned my water into a muddy mess.
I can only assume a lot of the treated water left over the spill way during the flood that followed.
After it clears up should I have them come back and fertilizes again ?

About all you can do is wait and see. Wait a week after the muddy water settles to see if a bloom begins, then add fertilizer in small amounts as/if needed.