File System Issues - Sony Xperia Z Ultra

I really need some assistance in understand this issue that i'm experiencing on my new XZU phone (not even 2 weeks old!).
I seem to be getting some odd file system issues wherein certain files which are supposed to be in a certain location (OBB folder) suddenly disappear. I've been researching and the general idea is that this is an Android KitKat issue but I posted here on the hopes finding a solution to this problem.
Some pointers regarding on what happened (note: phone is not ROOTED):
1. Installed game like Plants vs Zombies 2 (legit) and the OBB files were correctly placed on the OBB directory.
2. I also purchased Comic Rack full edition which seems to have created a Storage/Emulated directory on the root of my internal drive when creating a comic folder.
-- Initially i made the mistake of deleting this folder which deleted my whole file system (both internal and external sds). I already did a factory reset after this issue, but the obb movement issue as mentioned above still happened.
---- I noticed that some of the Comic files added by Comic rack through wifi syncing are added on the directory in the emulated section i.e (Storage/Emulated/SDCARD/0/Comics/) instead of just Comics/ . However using the android file explorer and the desktop windows explorer shows different files/locations.
------- I'm mentioning the Comic Rack issue because i suspect this might be related to the missing obb due to the folder linking/mirroring system for android (i only read about it so please don't quote me on this)
3. Uninstalling PVZ2 removes the game from the apps list but the files are still accounted for in the storage. Using clean master does not detect these missing files and using other File explorers doesn't show any other directories that may have these files.
4. I read on google that the files might be on Root/Media/SDcard/something but i can't access this directory due to file permission (unrooted)
5. Redownloading the PVZ2 data files, simply puts back the missing files and makes the game work again. However i am not sure until when the issue can or will happen again.
Would anyone be able to explain this issue? or better, if there is a solution? Thanks

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How the fudge did you modify the system files and folders in / direction if you are not rooted????
App data are and can be located in these directories
/data/data/
/data/dalvik-cache/
/storage/emulated/android/obb/
/storage/emulated/android/data/
=== if you have an memory card inserted ===
/storage/sdcard1/android/obb/
/storage/sdcard1/android/data/
=== if you have an memory card inserted ===
If you have root permissions. Look in these folders for traces of the app you have issues with and delete any related files. Reboot.
Other common methods is also to reboot in to recovery and clear cache and clear dalvik cache then reboot to system.
But without root permissions or a recovery I don't see many options for you than do than flash a .ftf file which includes the whole stock rom. If that works on locked bootloader...can't remember by now.

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SÜPERUSER said:
How the fudge did you modify the system files and folders in / direction if you are not rooted????
App data are and can be located in these directories
/data/data/
/data/dalvik-cache/
/storage/emulated/android/obb/
/storage/emulated/android/data/
=== if you have an memory card inserted ===
/storage/sdcard1/android/obb/
/storage/sdcard1/android/data/
=== if you have an memory card inserted ===
If you have root permissions. Look in these folders for traces of the app you have issues with and delete any related files. Reboot.
Other common methods is also to reboot in to recovery and clear cache and clear dalvik cache then reboot to system.
But without root permissions or a recovery I don't see many options for you than do than flash a .ftf file which includes the whole stock rom. If that works on locked bootloader...can't remember by now.
Click to expand...
Click to collapse
I'm also not sure how those files were modified because i dont have root permission. Comic Rack was somehow able to make the Storage/Emulated folder visible on windows and somehow messed up my file system (just a guess). I already looked at those directories (through windows) and they are empty. Those folders are not visible through android based file explorers on my phone

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ckenni2000 said:
I'm also not sure how those files were modified because i dont have root permission. Comic Rack was somehow able to make the Storage/Emulated folder visible on windows and somehow messed up my file system (just a guess). I already looked at those directories (through windows) and they are empty. Those folders are not visible through android based file explorers on my phone
Click to expand...
Click to collapse
You can not look in to these folders with a computer as android nowadays use MTP protocol to communicate with usb. You need to use ADB or a local file manager on your device like https://play.google.com/store/apps/details?id=com.speedsoftware.rootexplorer
To write files in sdcard1 without root permissions you need to mount the sdcard manually in a pc. Android has these functions disabled since not so long ago.
Remove the sdcard from the phone. Insert sdcard in a sdcard reader connected to your computer and open the folder.
If you are only read and write files in /storage/emulated/ you do not need root permissions as this is your personal storage space and you can use an app like this https://play.google.com/store/apps/details?id=com.estrongs.android.pop
Install this app and look in
/storage/emulated/android/obb/
/storage/emulated/android/data/
When you install es file explorer by standard the app starts in /storage/emulated/ directory so you only need to locate a folder called "android"
Screenshot on my device with ES file explorer started
{
"lightbox_close": "Close",
"lightbox_next": "Next",
"lightbox_previous": "Previous",
"lightbox_error": "The requested content cannot be loaded. Please try again later.",
"lightbox_start_slideshow": "Start slideshow",
"lightbox_stop_slideshow": "Stop slideshow",
"lightbox_full_screen": "Full screen",
"lightbox_thumbnails": "Thumbnails",
"lightbox_download": "Download",
"lightbox_share": "Share",
"lightbox_zoom": "Zoom",
"lightbox_new_window": "New window",
"lightbox_toggle_sidebar": "Toggle sidebar"
}

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I think i figured out the issue somehow. Just as a reference, if you guys used the Disk Usage APP, does your System Data show more than 4GB? Mine does and i assume these are the files that were previously on my OBB folder that were somehow transferred to the Root or System/Data of the phone that i am unable to access/delete.
Would there be a way to delete these files aside from rooting/factory reset

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ckenni2000 said:
I think i figured out the issue somehow. Just as a reference, if you guys used the Disk Usage APP, does your System Data show more than 4GB? Mine does and i assume these are the files that were previously on my OBB folder that were somehow transferred to the Root or System/Data of the phone that i am unable to access/delete.
Would there be a way to delete these files aside from rooting/factory reset
Click to expand...
Click to collapse
I don't know what that app is.
Apps installed in /data/app can not be moved to /system/app without root permissions unless it is a bloat app from either google or the manufacture ie samsung/SONY/LG etc
However app data and cache files can remain if there was an error with uninstallation or some error in the system.
Your only option if you don't have root permissions to access those folders is to do a factory reset or a reinstallation by flashing a stock .ftf rom