There was a time when the major font manufacturers had rules against supplying your licensed fonts to a jobber or service bureau ... expecting them to license their own copies to legally do the work. Those positions have been relaxed by most foundries and the only requirement most make is that you destroy the supplied copy when the work is completed.
In actual experience, we probably average less than one client a year wanting to supply their own special font. Most don't even know what they identify themselves with. The few that do, will be able to name it and sometimes even tell you where to get it.
In 23 years of sign making, I have never experienced what you are saying has or may happen. In any event, it is not your job to play copyright cop and your client's procurement habits should not be made part of your problems.