After I successfully set up a cloudflare r2 remote, I use it for one day, but later I found out that the mounted folder throw error, so I tried to remount it , but in
rclone listremotes
the r2 remote disappeared, and I checked the config file, it was indeed not there. I am using a encrypted config file, so it cannot be deleted manually. Also, I tried set up a webdav for filen.io before, but it also was deleted automatically after a some time, I could not figure out why. Is there any option to make rclone not delete config entry if the config entry is not valid for that time?
Nope. As it is not needed. Rclone does not delete config entries on its own.
You would be the first person ever claiming such thing. Which of course does not mean that you are wrong but rather that your conclusions are very unlikely.
What can be happening is that you are checking using different user than used to configure your remotes. Maybe sudo rclone listremotes works? Double check who are you running your account as.
If above is not the case than please provide a bit more info about your configuration and setup. Maybe some clues are there.