I have had this issue come up about about 4 times since I have been running CS6.
When I open a customers document everything is fine no errors. I save it the same way I do the rest of the 30 jobs a day. When I re open the fonts will not load. If I open the customers document again it is fine and all fonts work, this cause problems because all of th changes that have been done need to be redone, because the only way I have found to fix this is to save over it with a new copy of the customers files.
I am running CS^ creative suite on a intel 27" iMac OS 10.7.3
The file is being saved to a prinergy job server not sure what version of server software that is running. We have at least 30 jobs sometimes over 45 indesign jobs a day getting processed and it only seems to be a couple. I tried restarting indesign then the computer but no luck. If I have my troubled document open and the find font window open it shows that there are fonts not available, I then open the customers document and everythign is fine. With both documents open at the same time I can toggle between them and see the fonts are there for 1 but not the other.
Any help would be greatly appreciated.
Are you working with a Packaged file? If so, the problem is probably that youare moving the file out of the directory that holds the Document Fonts folder that is part of the package, or saving with a new name.