No. Sometimes package managers run into issues though. It's rare, but it's possible. If you had been updating on the CLI you would have seen the problem.

Anytime there is an update, files are often deleted during that process so they can be replaced with new files or because those files are no longer part of the new version being installed. If an error occurs during this process, it is possible that an application will appear not to be installed because it's broken.

Anyway, most software does at least partially "uninstall" when it is updating, so if the install fails, then it's always possible that an update will have uninstalled something. That's just updates regardless of operating systems, package managers, etc.

Actually, in the case of a web browser, Flatpak weakens both Firefox's and Chromium's internal sandboxing, possibly allowing for breaking of cross-site or site-host boundaries. Firefox is even weaker then Chromium as a Flatpak because it can't use the zypak fork server. Both are weakened, best to avoid.

For basically any other app, Flatpak can be beneficial as a sandbox.

Basically, don't sandbox browsers because its like wearing 2 condoms. The only sandboxing tool I know that doesn't interfere with the browser's sandbox (and also doesnt allow for the possibility of privilege escalation, like Firejail) is Bubblejail

PS: Since you mentioned you are on Fedora, Bubblejail is offered through this COPR repo from the Secureblue team. It provides a sandbox without interfering with the browser's sandbox. It comes with profiles for Firefox and Chromium. Only issue ive experienced is that the sandbox works, aka it means I can't access files from my home directory unless explicitly given permission to a folder.

What this person told you was wrong, you need to use flatpak run [package id] to run flatpak apps. You can do flatpak list to see all installed flatpaks with their ids. An id looks something like org.example.app and you'd run it with flatpak run org.example.app.

Also, is it shown as being installed in Discover? If it's not you could try just installing it again and if it is, you can try uninstalling it first. The user data for Firefox should stay intact.

Bash will cache command locations so it doesn't need to scan your path too frequently. You can clear it with "hash -r".

See the other comment about running flatpaks - it's their fatal flaw imho.

its flatpak run org.mozilla.firefox