Where were the fonts installed on your computer before you installed Lion? Did you do an install in place (rather than clean install)? You may have to replace them from a backup. You did do a backup before your Lion install, right?
I noticed when I did my Lion install that I had to replace a few things when folders were replaced in the install process.
Some were in Library/Fonts and another was in a folder in a folder in that Fonts folder.
So, they are where they always were. Just InDesign won't see the System/Fonts fonts and mine at the same time, while Illustrator continues to see both.
I know Adobe doesn't like to issue updates, but I sure with they would fix this in CS 5 again...
If InDesign doesn't see the fonts, put them in InDesign's Fonts folder: /Applications/Adobe InDesign CS5/Fonts.
Interesting trick, Steve. Thank you!
For what it is worth, here is what is happening now.
In Apple's Font Book, it appears that although both Helveticas are shown as on, that is, both are black text, the font with the yellow caution symbol is also listed as inactive (in the Information pane). So, it appears that Apple is attempting to resolve duplicates on its own and is using the user's fonts over their own.
In InDesign, I only have access to my fonts, not the System's duplicates. I suppose I could try making duplicates of the System fonts and putting them the InDesign font folder if I really wanted both...
In Ilustrator, I see two Helveticas listed, as I would want. But, only the first one sticks; that is, the check mark next to the font always remains on the top font, never allowing me to select the second font, from the Options bar. But! if I go to the main menu at the top of the screen and select Type > Font > Helvetica, I can choose either Helvetica, even though Font Book indicated that one is inactive.
Like I said, for what it is worth...
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InDesign uses its own font management, it doesn't use the OS's routines, so it's unsurprising tha there are diffrences.
Having multiple fonts with the same name is asking for trouble. You should probably rename your custom version of Helvetica.
Renaming the Helveticas might be a good idea. These are old postscript fonts. I suspect one would have to rename the screen fonts. They are licked in a Suitcase what I haven't been able to open for many versions of OS X. The Suitcase has a different name, but not the screen fonts inside.