I know this thread is old, but I thought I'd add how I got into this same situation in case someone else has the problem in the future, as the OP didn't seem to figure out how to get the apps back to re-add to the bottom bar.
I had this same problem but with the Messaging app. How I got there was I had gone to the menu > Applications > Messaging and hit Disable, then I hit Enable. This removed it from my bottom bar and just put it back into my full Applications list. The posting that mentioned that you have to go into the Applications screen to get it fixed was what worked for me getting it back into the bottom bar. But as I said, it appears the OP didn't see the apps in their full Applications list, so maybe they had disabled the app and never re-enabled it. At least that's what worked for me. Hope this helps someone else. Thanks for the clarification on how to get it back in the bottom bar.