You’re removing one of its depends (e.g. xdg-utils):
$ apt-cache show qubes-core-agent
Package: qubes-core-agent
Version: 4.2.26-1+deb12u1
Architecture: amd64
Maintainer: unman <unman@thirdeyesecurity.org>
Installed-Size: 729
Depends: apt-transport-https, dconf-cli, dmsetup, gawk, graphicsmagick, init-system-helpers, initscripts | sysvinit-utils, librsvg2-bin, locales, ncurses-term, psmisc, procps, util-linux, e2fsprogs, parted, python3-daemon, python3-qubesdb, python3-gi, python3-xdg, python3-dbus, qubes-utils (>= 3.1.3), qubes-core-qrexec, qubesdb-vm, systemd, xdg-user-dirs, xdg-utils, xen-utils-common, xen-utils-guest, xenstore-utils, python3:any, libc6 (>= 2.34), libqubes-rpc-filecopy2 (>= 4.1.7), dconf-gsettings-backend | gsettings-backend
Recommends: cups, gnome-terminal, gnome-themes-standard, haveged, libnotify-bin, locales-all, mate-notification-daemon, ntpdate, system-config-printer, qubes-core-agent-nautilus, qubes-core-agent-networking, qubes-core-agent-network-manager, x11-xserver-utils, xinit, xserver-xorg-core, xsettingsd, xterm
Conflicts: firewalld, pulseaudio-qubes (<< 4.2.0-1), qubes-core-agent-linux, qubes-core-vm-sysvinit, qubes-gui-agent (<< 4.1.6-1)
Homepage: https://www.qubes-os.org
Priority: extra
Section: admin
Filename: pool/main/q/qubes-core-agent/qubes-core-agent_4.2.26-1+deb12u1_amd64.deb
Size: 94476
SHA256: ea13bf510002a0b80f6d0acf226f90959eb20420d2bf3eefa7beb8d358f3205c
SHA1: 431c45ad5a3891260790cf798d158f4ddfab9465
MD5sum: 56b70ef04b1c4ff9e9df4fa75761c815
Description: Qubes core agent
This package includes various daemons necessary for qubes domU support,
such as qrexec services.
Description-md5: d5c21beb3c25cf7972d88fc97ad4fac4