How do you remove bad DNS server IPs from systemd-resolved?

You may use this command: sudo systemd-resolve --flush-caches or sudo resolvectl flush-caches (latter command taken from the man page of systemd-resolve)

To verify that flush was sucessfull, use: sudo systemd-resolve --statistics

Sample output:

Cache
  Current Cache Size: 0
          Cache Hits: 101
        Cache Misses: 256

Note also the section of the systemd-resolve manpage about /etc/resolv.conf, which mode are you operating in ?

/etc/resolv.conf

Four modes of handling /etc/resolv.conf (see resolv.conf(5)) are supported:

systemd-resolved maintains the /run/systemd/resolve/stub-resolv.conf file for compatibility with traditional Linux programs. This file may be symlinked from /etc/resolv.conf. This file lists the 127.0.0.53 DNS stub (see above) as the only DNS server. It also contains a list of search domains that are in use by systemd-resolved. The list of search domains is always kept up-to-date. Note that /run/systemd/resolve/stub-resolv.conf should not be used directly by applications, but only through a symlink from /etc/resolv.conf. This file may be symlinked from /etc/resolv.conf in order to connect all local clients that bypass local DNS APIs to systemd-resolved with correct search domains settings. This mode of operation is recommended.

A static file /usr/lib/systemd/resolv.conf is provided that lists the 127.0.0.53 DNS stub (see above) as only DNS server. This file may be symlinked from /etc/resolv.conf in order to connect all local clients that bypass local DNS APIs to systemd-resolved. This file does not contain any search domains.

systemd-resolved maintains the /run/systemd/resolve/resolv.conf file for compatibility with traditional Linux programs. This file may be symlinked from /etc/resolv.conf and is always kept up-to-date, containing information about all known DNS servers. Note the file format's limitations: it does not know a concept of per-interface DNS servers and hence only contains system-wide DNS server definitions. Note that /run/systemd/resolve/resolv.conf should not be used directly by applications, but only through a symlink from /etc/resolv.conf. If this mode of operation is used local clients that bypass any local DNS API will also bypass systemd-resolved and will talk directly to the known DNS servers.

Alternatively, /etc/resolv.conf may be managed by other packages, in which case systemd-resolved will read it for DNS configuration data. In this mode of operation systemd-resolved is consumer rather than provider of this configuration file.

Note that the selected mode of operation for this file is detected fully automatically, depending on whether /etc/resolv.conf is a symlink to /run/systemd/resolve/resolv.conf or lists 127.0.0.53 as DNS server.