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Help Damaged memory/filesystem?

My phone dropped while on, back over open and the battery popped out. basically turned off prematurely. At reboot strange messages from some apps (Swiftkey, whatsapp, go sms pro): apparently run out of memory (while 5GB still free on phone's memory.
Aftre some minor attempts I have formatted the SD and perfomed a factory reset, hoewever once reinstalled the apps, the problem is still there.
I have noticed that the factory reset will not wipe out the phone's memory as all the users folders are still there.
Could it be the phone memory filesystem got corrupt? In this case how can I format the phone's memory? My phone is rooted and got CWM installed. Maybe I could format the phone meory from bootloader and flash stock ROM from bootloader?
 
You will need to format the phone's Internal memory separately as described in Firmware update problems... what you can do!, which describes, in detail, how to Factory Reset and fully format both the internal and external memory as well as how to flash stock firmware.

Yes mate! Thanks! I have formatted the internal memory and the offending apps are back again working!

What I miss is what does the formatting! The SMS are still there and other app settings too. Shouldn't the formatting wipe out all the app's data?
 
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Yes mate! Thanks! I have formatted the internal memory and the offending apps are back again working!

What I miss is what does the formatting! The SMS are still there and other app settings too. Shouldn't the formatting wipe out all the app's data?

Are you sure that the apps and settings are not re-downloading from your gmail account if you have then sync'd to that?
 
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