Re: clean-up after upgrade.

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If you are able to boot with F29 last kernels without errors you might want remove old F2x kernels and their devel/module packages too.

dmesg|grep -iEw 'bad|bug|conflict|corrupted|error|fail|failed|fault|fatal|Lock|NULL|segfault|stack|trace|warn'

"uname -a" will tell you the release version of your booted kernel and what module version is needed for your nvidia card.
if I pick it right removing kmod-nvidia-5.0.7-200.fc29 could be a problem.
it seems 5.0.7-200 is the last released F29 kernel:
https://bodhi.fedoraproject.org/updates/?packages=kernel

to be save save the above output in a file, remove the above packages and play with your application if they are still running.
If not reinstall the needed packages.

maybe java could be the case if you are running java programs which need old java. 
install the old java packages and reconfigure your java with "alternatives --config java"

*I* usually do after an upgrade:
sudo dnf autoremove
sudo dnf distrosync

handle with care !

Q.'s: 
what does "@@commandline" mean ? 
kmod-nvidia installed by hand ?
is rpmfusion on your box enabled ?

https://rpmfusion.org/Configuration
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