There are options for you if the insurance company does not approve the replacement of your roof or siding.

If your contractor thinks the insurance company has overlooked the damage that exits, then the next step is to request a re-inspection.  All policy holders are entitled to two inspections by the insurance company.  If you are adamant, you can also insist on getting a new set of eyes on your property in case you don't feel you were given a fair assessment the first time around.

The insurance company may ask you to submit an estimate from your contractor in order to initiate the re-inspect process.  If you don't want to go through this, you can simply stand firm and demand a re-inspect.  

Always remember, you are the policy holder, you are the paying customer for your insurance company.  It is in your contract with the insurance company to give you two inspections if you are not satisfied with their initial assessment.