So basically it loads a save from the previous version of apk, is this correct?
You need to uninstall the previous version from the phone, before installing the new one.
If it still does this even after clean install, then maybe there is some auto-backup software on your phone that keeps app data after uninstalling? Like TitaniumBackup or something similar.
What I have done so far.
Removed all the checkpoints and its respective events.
Cleared the data/catch and uninstalled the previous apk and install the newly debugged version of the app.
but Still, the game began from the same old location HOW?
No, there is no backup kind of software I have installed.