I restarted my iPad this morning, everything is gone. Strange thing is, Cydia and the tweaks are still installed. I opened up iFile and it's showing my application data is still there along with movies and what not. Opened Cydia and it's showing that no tweaks are installed.
I haven't installed anything in a few months from Cydia, nor updated any tweaks in a few weeks, so I have no clue what is going on.
I'm currently away from my personal computer for the day, maybe someone can suggest a way to solve this issue.