rgheck sc
What I'd propose myself, somewhat along these lines, is that this error only be shown once per file per session, rather than globally turned off. Or perhaps the error dialog could have an option that would effectively mean: Disable the warning for this file. We could also put such an option into Document>Settings.
Maybe only slightly related to this. I just tried to compile the User's guide without having a PNG->EPS converter. I think I received approximately $\inf$ errors, which all wanted some sort of user input..
It would be nice that LyX would only show one error message for this.. Vincent