Random apps come up as "application not installed" on reboot. Can someone help me?

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Every time I reboot, more apps become "not installed" if I reinstall them they are uninstalled again on reboot. I am so frustrated and nothing I have researched on this subject is working.
 
I have a rooted Galaxy on5 running marshmallow; it has xposed framework installed with several modules active and custom key settings . Is there anyway to backup and restore all of this without losing any of the effort I put into this? Or possibly a solution that doesn't involve a factory reset?
 
Upon further inspection it seems that every application affected was installed onto the sd card at one time. I have deleted all associated files from the sd card including from .androidsecure using a computer and there is no difference. I also have tried ejecting the sd card and testing if the error still occurs without it and it does. I did root following instructions on xda, but no one else is having this issue. I'm going to go through the stuff I've done. I have had multiple write2sd fix methods active (not at the same time) these methods are disabled now. I had xposed framework installed (which is currently uninstalled, also tested while uninstalled and the error still occurs). I've also made attempts to uninstall knox from my device though I'm not sure if I succeeded. I also have made attempts at setting selinux to permissive (pretty sure I succeeded using a terminal emulator) in order to get certain gamepads to work on this device (didn't succeed here). How do I clear system cache? I have TWRP recovery installed.
 
Are you using the "Move to SD" feature for apps? That's generally not advisable, since SD cards are inherently unreliable, which can lead to app crashes and data loss.
 

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