I'm at a loss, then. I've been running Yosemite for about four months now and have never encountered any font problems nor read of any problem like you're having. I've no idea why it happened or what could have caused it to happen. Do you have backups of your old Fonts folders? Pulling them from backups is the only way, short of installing each fonts again, that I know of to remedy the situation.
Sorry that I was no help.
Clinton
MacBook Pro (15” Late 2011), OS X Yosemite 10.10, 16GB Crucial RAM, 960GB M500 Crucial SSD, 27” Apple Thunderbolt Display