Packages/libraries missing (MESA 3D) after removing Flatpak

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Hi,
Because I had a problem with opening Jupii (a permissions error, user 1000), I found a solution removing and reinstalling flatpak (from here: Flatpak app suddenly stopped running - gives permission error - Flathub Discourse)
I copied the files that would be removed and installed the ones I needed again. All seems fine. Except, these are the files still missing:

Fedora Platform            org.fedoraproject.Platform           39           f39         fedora   system\
Freedesktop Platform       org.freedesktop.Platform             22.08.23     22.08       flathub  system\
Freedesktop Platform       org.freedesktop.Platform             23.08.14     23.08       flathub  system\
Mesa                       org.freedesktop.Platform.GL.default  24.0.3       22.08       flathub  system\
Mesa (Extra)               org.freedesktop.Platform.GL.default  24.0.3       22.08-extra flathub  system\
Mesa                       org.freedesktop.Platform.GL.default  24.0.3       23.08       flathub  system\
Mesa (Extra)               org.freedesktop.Platform.GL.default  24.0.3       23.08-extra flathub  system\
Intel                      org.freedesktop.Platform.VAAPI.Intel              22.08       flathub  system\
Intel                      org.freedesktop.Platform.VAAPI.Intel              23.08       flathub  system\
openh264                   org.freedesktop.Platform.openh264    2.1.0        2.2.0       flathub  system\
Freedesktop SDK            org.freedesktop.Sdk                  22.08.23     22.08       flathub  system\
TeX Live Sdk extension     …g.freedesktop.Sdk.Extension.texlive 20210325     23.08       flathub  system\
Breeze GTK theme           org.gtk.Gtk3theme.Breeze             6.0.3        3.22        flathub  system\
KDE Application Platform   org.kde.Platform                                  5.15-23.08  flathub  system\
KDE Application Platform   org.kde.Platform                                  6.6         flathub  system\
QGnomePlatform             org.kde.PlatformTheme.QGnomePlatform              6.6         flathub  system\
KDE Software Development … org.kde.Sdk                                       6.6         flathub  system\
QAdwaitaDecorations        …ylandDecoration.QAdwaitaDecorations              6.6         flathub  system\

Some seem important. For instance, the mesa stuff prevents me from opening the Nextcloud Password Manager.
How can I reinstall that? And which other things are important to reinstall?

I find some info here: che/mesa Copr (and here: Precompiled Libraries — The Mesa 3D Graphics Library latest documentation). But I’m afraid to f*ck things up.

I already did sudo dnf install mesa-*