Memory reading issues, both internal and external

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Android Central Question

Sony Xperia M5, Android 6.0.

Random files show 0 kb on the sd card if I try to read them using a Windows 10 PC connected with USB cable. Some folder wont show up at all and if I delete or add folders using my phone they wont show up on the PC.

If I directly plug in the SD card to my PC (SD card reader) without my phone in between the files show correctly file size and if I copy or cut them to my PC they are still functional (mp4 and srt) but if I try to copy or cut them while the SD card is inside the phone the 0 kb files will stay 0 kb, even after moved to the PC's hard drive.

If after I have copied files from the SD card to my PC using the SD card reader and insert it back inside my phone applications no longer start. Clearing cache does not fix it, I must either delete all data or fully reinstall the application to get it working again.

And sometimes (very rarely) the applications on my internal memory just says they cannot be launched anymore and I must clear all data from those as well.

Backup using Sony Companion PC software wont function properly (failed applications [some], images [all] and videos [all]) if the phone has 2 GB or less internal memory left, it only worked when I had 4 GB free space. The PC software only told me on the third day trying to back it up that it was running low on memory, the phone itself never told me that it was running low on memory.

I have done a Software Repair from Sony Companion PC software and didn't restore any back ups, not from PC and not from Google Drive and the problem still persists.

Why is the phone having trouble reading both internal memory and external memory?
The SD card and the application which generates both mp4 and srt files to the memory work normally on another phone. The SD card is fully functional with no bad sectors etc. tested with Windows 10 chkdsk.

Also tried another Windows 10 PC, another USB cable, another SD card, the problem only existed on this one phone but not on another phone running same Android 6.0 OS (different brand).

This problem is new and didn't occur until now, ~13 months later using the phone, application and SD card.

The phone did corrupt the SD card about 2 months ago, I did format the SD card first using Windows 10 and then the phone, now it should work normally and does on another android phone and Windows PC.

Help, what's wrong with my phone?