After running some experiments I have finally managed to solve this issue for my Paperwhite4.
For anyone having the same issue - follow this sequence:
Take a side loaded document of any format
Open it w Calibre
Right click on it and press “Edit metadata”
In a new window press the button “Download metadata” (it’s at the bottom of the screen)
Follow thru with ...
No. I don't think it's because of your kindle discharged to 0. Many times my kindle also goes to Zero percentage but it connected to wifi again once I charge my kindle. If you can reset your kindle I think it might solve your issue. Please find the link to how to Reset your kindle.