I work for a printing company, as well, and I'm having a similar issue. InDesign is prioritizing the Adobe Font (which is deactivated) rather than the packaged font, and at times it will interfere with the fonts and give me a message that the fonts are missing. I can save and close, and sometimes when I reopen the fonts will magically be there, and other times it will say missing again. It seems to be fairly random, but the only thing I can trace it back to is the Adobe Font. When it's missing, the Adobe Font menu always pops up asking if I want to activate it (though activating it doesn't work, and it still shows as missing after activation). I have "Auto-activate Adobe Fonts" turned off, but it doesn't stop it from trying to look for them if it deems they are "missing."
I work for a printing company, as well, and I'm having a similar issue. InDesign is prioritizing the Adobe Font (which is deactivated) rather than the packaged font, and at times it will interfere with the fonts and give me a message that the fonts are missing. I can save and close, and sometimes when I reopen the fonts will magically be there, and other times it will say missing again. It seems to be fairly random, but the only thing I can trace it back to is the Adobe Font. When it's missing, the Adobe Font menu always pops up asking if I want to activate it (though activating it doesn't work, and it still shows as missing after activation). I have "Auto-activate Adobe Fonts" turned off, but it doesn't stop it from trying to look for them if it deems they are "missing."