The assessor's office advised us to use the land value as stated on the property tax bill for the land value on the form before and after the fire, since there was no contamination of soil or anything else that would affect the land value.

If any contamination is found, most likely will require clean up and sign off from state environmental authority.

Well today it was announced that the EPA has found lead contaminated ground.

Are there now mold issues or other contamination due to the water intrusion?

If you order an environmental and find out there was a gas tank that was never removed under your 16 unit apartment building you will immediately be liable for any damage from contamination moving forward (an extreme case but it illustrates the point). 

I did not see any barrels containing who-knows-what contaminants inside the building. 

If there's existing contamination, cleanups can be catastrophically expensive. 

So even elements that don’t appear damaged can be contaminated.

It’s a 3 family in a good location and the numbers work for me but during my inspection today the inspector asked if it had a clean E21 report to certify that there were no contaminates.

Black mold is like any other household growth/contamination...it doesn't come back unless the conditions that caused it come back...did the remediation company give you a certificate or warranty?