I had the same problem with my RT-AX88U. I decided to try to script the changes I wanted to keep in the hope that they would persist during reboots. Mine was only disappearing after reboots. I connected with a terminal to check whether my jffs partition was writeable or not. After doing a...
Try going to "Administration - Firmware Upgrade" and select "Upload" from "Manual firmware update : Upload". I think you might be trying to load firmware in a location that expects a configuration file under "Administration - Restore/Save/Upload Setting".