Have you read this section of my article? Scroll down a bit to the subheading, Removing Helvetica, Helvetica Neue and Helvetica Light in Leopard through Mountain Lion.
Though, when I remove the font Applications such as InDesign, Quark and the MS Office suite will no longer recognize any other font that is not located in the System/Font folder.
That shouldn't happen. All apps should still see any and all other active fonts on the system.
If you launched Font Book after the safe mode startup to clear Font Book's database, it will have created another database. Any damaged fonts on the system will typically corrupt Font Book's database, which in turn often causes the issue of some apps seeing available fonts, but not others.
If Font Book is still off the system, then do a safe mode startup again to ensure its database is gone. Then follow these steps to remove all font cache data from the system.
Close all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:
sudo atsutil databases -remove
Terminal will then ask for your admin password. As you type, it will not show anything, so be sure to enter it correctly.
This command removes all font cache files. Both for the system and the current logged in user account. After running the command, close Terminal and immediately restart your Mac.
This may, or may not help, but it will ensure that Font Book, its database, and font cache files are taken out of the equation.
You could invest in Suitcase Fusion. When you enable your Type 1 PostScript fonts, it automatically disables the OS X system versions of the fonts. When you turn off the T1 PS fonts in Suitcase's interface, the system fonts are turned back on.
If you don't really want to trust an automatic system, then follow the steps in my article to remove the backup versions of Helvetica from the deeply buried ProtectedFonts folder. Once you've done that, then:
1) Copy Helvetica.dfont and HelveticaNeue.dfont from the /System/Library/Fonts/ folder to a new location. It doesn't matter where, other than not to another one of the Fonts folders. You could create a folder at the root of thedrive named "System Helvetica fonts" and put them in there. Once you have the copies in place, delete those fonts from the System folder.
2) Create a second folder next to the first for your Type 1 PostScript fonts and aptly name that folder.
3) Using Suitcase Fusion as an example, now drag and drop those two folders onto the Font Library heading. Two sets will be created with the same names as each folder. Personally, I always use Suitcase with the preference to Add fonts leaving them in place. I've never seen a real purpose for adding all fonts you install to a separate Vault database.
4) You now have the system and T1 PS fonts in their own sets and can turn them on and off manually as needed. Turn the system fonts off and the T1 PS fonts on when required for your client work, and reverse which is on/off otherwise.
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