SFTP SSH authentication stopped working with ssh-agent on macOS

[kataba]

I recently set up SSH access to my web servers on my Mac by following GitHub's documentation for Generating a new SSH key and adding it to the ssh-agent. After that, I installed FileZilla and the connections to my servers worked correctly. However, today I restarted my Mac, and tried to connect via SSH using the terminal, it asked me for the passphrase of my private key. I entered it and could connect. However, I still couldn't connect to my servers via SFTP on FileZilla. I tried running eval "$(ssh-agent -s)" and ssh-add --apple-use-keychain ~/.ssh/id_ed25519, but this did not help. I am either getting in FileZilla:

FATAL ERROR: No supported authentication methods available (server sent: publickey,gssapi-keyex,gssapi-with-mic)
Error: Could not connect to server
or

Status: Using username "root".
Status: Access denied
Error: Authentication failed.
Error: Critical error: Could not connect to server
depending on which server I try to connect to.

If I make use of FileZilla's key import, converting the key file to a supported format (.ppk extension), and manually entering the passhprase in the prompt, the connections succeeds.

Why did FileZilla stop making use of the ssh-keygen (which is used fine through the terminal when using the SSH and SFTP protocols)?

Debug log excerpt:

Trace: Pageant is running. Requesting keys.
Trace: Pageant has 0 SSH-2 keys
I have always had "Normal" Logon type and echo $SSH_AUTH_SOCK prints /var/folders/sm/xxxxx/Tssh-xxxx/agent.1133, as described here. I've tried using both Normal and Interactive mode, and both don't work anymore, but they used to work before the system restart. I also tried restarting my system again and this didn't help.

Removing FileZila preferences, removing the app and reinstalling it did not help.