Yes you can. Let’s Encrypt’s HTTP-01 challenge imposes no requirement to keep the validation files around. Once you have the certificate, it’s done (the files in .well-known/acme-challenges are only there to prove to Let’s Encrypt that you control the web server; TLS clients do not use them to “guarantee the security” of encryption).
You should check if there’s an option in the server management plugin to “clean up challenges” or something along those lines. Otherwise I would ask your hosting provider or the plugin vendor - this is buggy behavior that should be fixed.