The highest your market will bear... considering any competition you have (if any).
The problem is, even the trivial changes require laying out and cutting an add-on PCB.
If I were you, I'd charge per hour (and materials) if this is a custom one-off job.
or
Once you know the total, offer to give them a discount but with the condition the custom job they hired you to do, you can re-sell to others.