We normally handle this one of two ways. Simply duplicate the impressioned key and give to the customer, sometimes we duplicate with a sheet of paper under the filed key and fine tune by hand.
The other way is to use the known depths and spaces of the lock but go 1/2 a cut shallow and use the code machine to adjust any cuts that are marking.
This takes up any wear of the pins and provides the best working key.
All this provided the cylinder does not come apart, if it does and is a pin tumbler lock we have a special machine that cuts a key based on the actual pins in the lock. It is very simple. The cylinder and pins are clamped into a jaw and a blank is inserted, a wire holds the blank in place. Now the pins are pushed up above the shear line. Now a blank is loaded in the other jaw. The cutter and the feeler pivot on an axis and as the feeler is placed over each pin it cuts that depth in the blank.