Steps to reproduce the issue

Click Update Structure in Joomla 4

Expected result

Composer provided libraries in libraries/vendor are untouched !

Actual result

FTP reveals two files get deleted.. Thats because they are listed in com_admin/script.php

/var/www/html/libraries/vendor/paragonie/sodium_compat/src/Core32/Curve25519/README.md
/var/www/html/libraries/vendor/typo3/phar-stream-wrapper/composer.json

Thu Apr 22 17:51:04 2021 [pid 75859] CONNECT: Client "::ffff:127.0.0.1"
Thu Apr 22 17:51:04 2021 [pid 75858] [www-ftp] OK LOGIN: Client "::ffff:127.0.0.1"
Thu Apr 22 17:51:04 2021 [pid 75860] [www-ftp] OK DELETE: Client "::ffff:127.0.0.1", "/var/www/html/libraries/vendor/paragonie/sodium_compat/src/Core32/Curve25519/README.md"
Thu Apr 22 17:51:04 2021 [pid 75860] [www-ftp] OK DELETE: Client "::ffff:127.0.0.1", "/var/www/html/libraries/vendor/typo3/phar-stream-wrapper/composer.json"

System information (as much as possible)

Additional comments