Fix/Workaround: losing 2FA config when configuration when updating profile with "Time Based One-Time Password (Google Authenticator)" 2FA enabled

fix-init.php

<?php
/**
 * Fix/Workaround for two-factor option issues.
 */

namespace Fix;

require_once __DIR__ . '/two-factor-totp-fix.php';
Two_Factor_Totp\bootstrap();

two-factor-totp-fix.php

<?php
/**
 * Two-factor options customisation. 
 * 
 */

namespace Fix/Two_Factor_Totp;

use Two_Factor_Totp;

/**
 * Startup.
 */
function bootstrap() {
  
  add_action( 'admin_init', __NAMESPACE__ . '\\update_2fa_otp_option' );
  
} 

/**
 * Override default 2fa otp option.
 */
function update_2fa_otp_option() {

	remove_action( 'two-factor-user-options-' . Two_Factor_Totp::class, [
		Two_Factor_Totp::get_instance(),
		'user_two_factor_options',
	] );

	add_action( 'two-factor-user-options-' . Two_Factor_Totp::class, __NAMESPACE__ . '\\two_factor_otp_option' );
}

/**
 * Display TOTP options on the user settings page.
 * Note: As per default two-factor otp behaviour when user profile is updated
 * with hitting enter key, the reset key submit will also get it submitted and
 * that submit the "two-factor-totp-delete" value as true, moving this to checkbox
 * resolves the issue of setting delete/reset flag on form submission on enter key.
 *
 * @param \WP_User $user The current user being edited.
 */
function two_factor_otp_option( $user ) {

	if ( ! isset( $user->ID ) ) {
		return;
	}

	$totp_instance = Two_Factor_Totp::get_instance();
	$key           = $totp_instance->get_user_totp_key( $user->ID );

	if ( empty( $key ) ) :
		$totp_instance->user_two_factor_options( $user );
	else :
		wp_nonce_field( 'user_two_factor_totp_options', '_nonce_user_two_factor_totp_options', false );
		$totp_instance->admin_notices();
		?>
		<div id="two-factor-totp-options">
			<p class="success">
				<?php esc_html_e( 'Secret key configured and registered.', 'al-jazeera' ); ?>
			</p>
			<p>
			<p>
				<input type="checkbox" name="two-factor-totp-delete"/><?php esc_html_e( 'Check here and click on reset key.', 'fix-two-factor-totp' ); ?>
			</p>
			<p>
				<input type="submit" class="button" name="two-factor-totp-delete-btn" value="<?php esc_attr_e( 'Reset Key', 'fix-two-factor-totp' ); ?>"/>
			</p>
			<em class="description">
				<?php esc_html_e( 'You will have to re-scan the QR code on all devices as the previous codes will stop working.', 'fix-two-factor-totp' ); ?>
			</em>
			</p>
		</div>
		<?php
	endif;
}

Issue ref: WordPress/two-factor#341

2fa otp reset key option was removing key on form submission with setting two-factor-totp-delete on submit button itself. Because of this everytime we update user profile by just hitting enter it find first submit button ( which is two-factor-totp-delete ) and submit form, which results in removing 2fa otp key and reset even when not needed.

As part of this fix we have moved two-factor-totp-delete field as checkbox and now it will only remove if checkbox is checked.