How did you reconfigure the virtual chassis, simply deleting configuration when virtual chassis created does not remove virtual chassis. It all depends on configuration method you adopted, pre provisioned or dynamic .
For dynamic method use following method.
request system halt member x
request virtual-chassis recycle member-id x
I think it will remove all alarms for faulty line card and if pre provisioned method use following technique
request system halt member x
configure
delete virtual-chassis pre-provisioned member x