I have been having this bug in Gnome 46, Fedora 40
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I don’t see any relevant change on this in Fedora 40.
You can always change the behavior with Preseve working directory to Always.
I think this depends on some shell script to adjust the prompt to tell VTE what the current location of the shell is. Did you maybe change your shell from bash to something different or have you modified your bashrc or profile to override the prompt command? Or did you somehow disable the code that sources scripts from /etc/profile.d?