I seem to have a problem with internet connectivity. I use NetworkManager with Proton VPN on an Arch KDE system. The wifi and VPN stay connected, but every once in a while the upload and download rates will go down to, at most, a few hundred KiB/s. The issue can be solved temporarily by disconnecting and reconnecting the VPN, but as I’ve had a similar issue without the VPN before, I do not know whether this is a VPN issue or a NetworkManager issue.
Proton on Linux is annoying to say the least. I've got it mostly working on my distro and without a DE. Have you checked the protovnpvn_reconnector service, assuming you're on systemd? It's kind of odd that it just slows to a crawl but maintains connection.