If someone else faces that problem with Silverblue or another immutable variant, here are the steps I took to revert to mutter-48.2-2 (the version before the bug):
First, I downloaded the commit history of the last 10 days
Then I checked the differences day by day and found the commit from May 26 to contain the older mutter version.
rpm-ostree db diff 71a337e442a2dc36df79e123bb5011a1ffc5e2bd0ce8aac61157fd6ecd477491
After that, I downgraded my system with rpm-ostree deploy 71a337e442a2dc36df79e123bb5011a1ffc5e2bd0ce8aac61157fd6ecd477491 and pinned the deployment with sudo ostree admin pin 0 so I would have a working system until the fix is published.
The patch was discovered to be incomplete. It fixes the mouse cursor issues, but application windows can still become invisible. GNOME will most likely be reverting the entire original bug instead of trying to patch it for now.
GNOME are preparing a 48.3.1 hotfix here, but it hasn’t been updated yet after the discovery that the patch was incomplete:
The Mutter 48.3-2 package should be available on all package mirrors now. It resolves the issue by reverting the code that caused the bug. This approach is also the most likely course of action for the GNOME project, and given the circumstances, we decided not to delay implementation any further.
I might make a separate topic for my situation in case it’s different from yours, but I am using Fedora Workstation on GNOME 48.2 (System is up-to-date) and I’m having issues with most if not all Electron-based Flatpaks (in my case Signal and FreeTube refuse to open. Signal shows a blank screen, FreeTube shows nothing). I have the latest version of mutter installed ( mutter-48.3-2.fc42).
I don’t appear to have this issue if I use a native RPM (I tried FreeTube’s RPM and it works just fine, compared to it’s flatpak which still just doesn’t function)
Okay, so, after a system update that didn’t update mutter (I checked), the issue is somehow resolved. Electron flatpaks work again.
But I’ve already migrated all of my Electron flatpaks to their native versions (For FreeTube I now use their RPM, for Signal I use a Debian distrobox) and those already worked flawlessly before the Electron flatpaks got fixed with a fairly recent update for me (And migrating data to them was as simple as knowing the right locations to copy and paste from).
All in all, this situation somewhat damaged my trust in Fedora Workstation as a stable distro that I can rely on not to break, but now I at least know how to install programs in a more reliable way (I’ll at least try to avoid flatpaks for apps built with Electron now).