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Local Security Policy
There are firewall settings that don't change when new programs modify windows advanced firewall. These rules sit beneath and supersede the main windows advanced firewall rules.
Type here to search-> "Local Security Policy" -> Click Local Security Policy.
There is a folder Windows Defender Firewall, with the same layout. Put your rules in here and they won't change, and they override the other rules.
I have also found out that these rules can be scripted by the command netsh, so I might make something later on.