Our Insurance Company denied our claim due to improper work being done on our roof, years before they became our Insurance Company.

Homeowner insurance covers sudden and accidental damage to your home. It does not cover a loss that occurs over a period of time, such as wet or dry rot. In addition, there is a specific exclusion for damage caused by faulty construction. In your case it sounds like the roofer took shortcuts and did not properly install the flashing, or install it at all, when they replaced your roof.If the roofer is still in business you should contact them about the damage to your home. It is likely their insurance company will deny the claim so you may have to file a lawsuit against them.It is always best to have your roof examined on a regular basis. Also, insurance companies often inspect a home before they will insure a home. However, it is unlikely they would have caught this omission, since the town inspector apparently missed it too, when the roof was done.