But I struggle to remove features like this:
d__Eukaryota;;;;;__ (only general taxa)
without removing all features like this: d__Eukaryota;p__Apicomplexa;c__Conoidasida;o__Coccidia;f__Eimeriorina;g__Cystoisospora
If you want to remove general taxa, you can use the command so it keeps only annotations with at least a given taxonomic level. For example, if you want your annotations to have at least the phylum level (i.e., we don't want annotations that only say d__Eukaryota;;;;;;, or d__Eukaryota;p__;;;;;), you can do something similar to:
The qiime taxa filter-table command allows you to be creative with your filters. There are parameters like --p-mode that you may find helpful in further filtering. You can check the official documentation for more info. Moreover, here you can find more useful tips and use cases.