waste due to flooding

It sounds like all the materials are going into the waste stream, so they would all need to be tracked for whether they were landfilled or diverted. If the volume of damaged material that you have to send to landfill is going to be high enough to potentially affect your LEED achievement, you might want to contact GBCI and ask about a possible exception - as a reviewer I spoke with a couple project teams that had materials stolen from a dumpster and we figured out a workaround. Just document the weight/volume as well as possible so you have a number to work with.

While I think that Emily's answer follows the LEED letter of the law and might be the black-and-white response, I also think that this is a bit of a grey area due to the special circumstances of the flooding. 

It would be easiest and the most straightforward to just include both the stored and replacement materials in your waste calculations. Yet I understand this could be detrimental to your diverted rate as I suspect there is not much that can be recycled/salvaged (as Emily noted). If the credit achievement comes into jeopardy because of these materials, you might want to use the Special Circumstances box on the credit form and explain your situation - stating what you included and did not include for example and why. Using Special Circumstances is a tool that you can never go wrong by using. 

Kay - It would be great if you could share the final outcome of your experience so we can all learn from it.

Totally agreed on the special circumstances narrative - use it anytime your project doesn't fit neatly into the LEED boxes! I do think this waste should be acceptable to exclude from your total as there simply is no reuse opportunity due to contamination beyond your control - just document what was damaged and disposed of the same way you've been tracking other waste streams.