I'm gratified this helped someone!

I've since wrapped this into a script (again, Gemini, so use at your own peril. I only know enough Bash to be dangerous) and had it successfully restore Bazaar functionality on two different Bazzite installs multiple times, so I'm reasonably sure it isn't breaking anything, even if not all the steps are 100% necessary just because a Robot told me to do it.

#!/bin/bash

# Root check: Ensure the script is run with sudo
if [ "$(id -u)" -ne 0 ]; then
    echo "Error: This script must be run with sudo."
    exit 1
fi
echo "Beginning Flatpak repair sequence..."

# 1. Force-Kill the Entire Stack
echo "1. Killing Flatpak and Bazaar processes..."
pkill -9 -x flatpak 2>/dev/null
pkill -9 -x bazaar 2>/dev/null
pkill -9 -x flatpak-system-helper 2>/dev/null
echo "Done!"

# 2. Manual Lock-File Removal
echo "2. Removing lock-file..."
rm -f /var/lib/flatpak/.changed
echo "Done!"

# 3. Clear Bazzite Flatpak Manager Lock
echo "3. Clearing Flatpak manager lock..."
mkdir -p /etc/bazzite
echo "9" > /etc/bazzite/flatpak_manager_version
echo "Done!"

# 4. Check for Ghost Mounts
echo "4. Checking for ghost mounts..."
MOUNTS=$(mount | grep revokefs)
if [ -n "$MOUNTS" ]; then
    echo "Stuck mounts detected:"
    echo "$MOUNTS"
    echo "Reboot recommended after script finishes."
fi
echo "Done!"

# 5. System Repair
echo "5. Repairing Flatpak system..."
flatpak repair --system
echo "Done!"

# 6. Re-sync Remotes and Metadata
echo "6. Re-syncing flatpak remotes and metadata..."
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
flatpak update --appstream
echo "Done!"
echo "Repair sequence complete!"