The same happened with Make by Theme Foundry.
This plugin was causing the following PHP Fatal error:
PHP Fatal error: Uncaught Error: Class 'WP_Application_Passwords' not found in /nas/content/live/yystaging/wp-includes/user.php:316
Stack trace:
#0 /nas/content/live/yystaging/wp-includes/user.php(469): wp_authenticate_application_password(NULL, 'wwww', 'xxxx')
#1 /nas/content/live/yystaging/wp-includes/class-wp-hook.php(287): wp_validate_application_password(false)
#2 /nas/content/live/yy1staging/wp-includes/plugin.php(212): WP_Hook->apply_filters(false, Array)
#3 /nas/content/live/yystaging/wp-includes/user.php(2982): apply_filters('determine_curre...', false)
#4 /nas/content/live/yystaging/wp-includes/pluggable.php(70): _wp_get_current_user()
#5 /nas/content/live/yystaging/wp-includes/capabilities.php(668): wp_get_current_user()
#6 /nas/content/live/yystaging/wp-content/themes/make/inc/error/collector.php(51): current_user_can('install_themes')
#7 [internal function]: MAKE_Error_Collector->__construct(Object(MAKE_API))
#8 /nas/content/live/yystaging/wp-content/themes/make/inc in /nas/content/live/yystaging/wp-includes/user.php on line 316, referer: https://yystaging.wpengine.com/
Then it reset all the theme customizations in the database.
This is on WordPress 5.6.1