I Posted the question because it took some time testing and wanted to spare you guys the trouble. This was my fix. This problem happend on a linux distribution.
You should indeed also update the conda environment.
So in the give qiime2 .yml file on https://docs.qiime2.org/2022.8/install/native/#install-qiime-2-within-a-conda-environment there exist a package which gives trouble.
Go into the yml file and remove the following package/line from the file before making an conda environment of it:
- bioconductor-genomeinfodbdata=1.2.7
After making the environment you have to manually add the package with:
conda install -c bioconda bioconductor-genomeinfodbdata
This will install the same version but without the extra problems.