Long story short, I had purchased new games since loosing my PS+ subscription and chalked up many hours in them (LBP1 and 2) they were not saved in PS+ online storage but they were on my PS3s internal storage. After re subscribing to PS+ the network seemed to decide for me that my old save files that were for old games were more important then my new saved files of new games and deleted them without asking me.
I realize that it's my own darn fault for not backing up these saved files but I don't think that deleting new saved files of Game A and replacing with old saved files of Game B should be a feature of PS+. Does anyone have or know of a way around getting these files back?
Playstation Plus supports automatic upload of PS3 save data (for compatible games) to online storage, but there was never any automatic download of save data from online storage. Playstation Plus won't replace save data on your PS3 hard drive with the online copy without prompting you, and will only do so if you manually copy it using the option menu. Online storage has its own folder which appears at the top of the PS3 Save Data Utility, but your local PS3 save data is also in the Utility further down in the list. You might need to scroll down to see it. You are probably looking at old LBP1 and 2 save data that was automatically uploaded to online storage the last time that you subscribed to Playstation Plus.
Unfortunately I resubscribed to PS+ to get my old save file of FFXIII but I found out that I had not uploaded it, nor had I backed it up. Good thing I wasn't any more then 2ish hours in to the game.