Checking Fonts for corruption
At this point, I don't know if you have an efficient solution. There are apps that will "check" fonts, but I don't that any of them checks for ALL possible problems.
Is there any pattern to the problems? Does it always happen when certain fonts are in a do***ent? Does it never happen when certain fonts are in a do***ent?
Other than doing an ****ysis like this, the only "general solution" I can suggest is spending a good portion of a day replacing all the fonts from original disks. And then, once that's done, make a copy of the folder(s) with all the newly installed fonts on a DVD or tape or anotehr HD (depending on what you have available for backup) so that if you ever have doubts about fonts again, you can replace all of them in one fell swoop at the cost in a realtively short time.
What I'm sure you're looking for is some utility that you can run that will examine all your fonts and decree each to be "ok" or "flawed." And do it in a reliable way, so you can depend on its judgment and replace only those it says are corrupt.
I think we'd all like that, given InDesign's hypersensitivity to font problems, but I'm pretty sure no such utility exists. (As I said previously, there are utilities that check fonts, and I've used them, but have found that some fonts the utilities said were okay actually weren't -- and vice versa.)
Other's mileage may vary, but that's been my experience, FWIW.
Don
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