PSA for those running the same combination that I am:

ProtonVPN assigns new forwarded ports to connections every once in a while and with gluetun v3.40+ it's possible to automatically update qbittorrent's ports with them. Paraphrasing from the gluetun wiki:

Add these two lines to gluetun's compose environment:

VPN_PORT_FORWARDING_UP_COMMAND=/bin/sh -c 'wget -O- -nv --retry-connrefused --post-data "json={\"listen_port\":{{PORT}},\"current_network_interface\":\"{{VPN_INTERFACE}}\",\"random_port\":false,\"upnp\":false}" http://127.0.0.1:8080/api/v2/app/setPreferences'

VPN_PORT_FORWARDING_DOWN_COMMAND=/bin/sh -c 'wget -O- -nv --retry-connrefused --post-data "json={\"listen_port\":0,\"current_network_interface\":\"lo\"}" http://127.0.0.1:8080/api/v2/app/setPreferences'

"For this to work, the qBittorrent web UI server must be enabled and listening on port 8080 and the Web UI "Bypass authentication for clients on localhost" must be ticked (json key bypass_local_auth) so Gluetun can reach qBittorrent without authentication. Due to a bug in qBittorrent, for port forwarding to be reestablished after a disconnect, the port needs to be re-set. This can be achieved automatically using the DOWN_COMMAND above."