If a feature will be really onerous to insert, discuss alternate ways of implementing it. Another option the customer has is to not add the feature if it causes undue burden on the software. I view existing software as a corporate asset. As with any other asset, you're always trying to protect its value. If a feature threatens to turn some software into a plate of spaghetti, inform the customer of the future ramifications of spaghetti code.
Most customers appreciate such candor.
A great customer understands that all changes cost money. Find the location in the code. Change the source code. Compile and link the revised code. Burn a ROM or microcontroller with the new code.