files in /etc/profile.d/ not run. No brew, no Flatpaks.

Hi all, I have a problem. None of my flatpaks appear on desktop, search, app launcher.
Pretext: I was wondering why all the documentation was saying we are using brew now, but there was no installation instructions and brew didn't seem to be installed on my system.
I found out I could get brew by adding "source /etc/profile.d/brew.sh" into my .bashrc or .zshrc and I did and it works.
But now all my Flatpak apps dissapeared from the desktop, quick launch etc. I can still run them manually with the "flatpak run .." command.
There also seems to be a /etc/profile.d/flatpak.sh script which apparently sets the environment variable where flatpaks should be found.
Maybe that is also not run for some reason? Can some one help me out?
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