Hi Lorenzo,
The latest CHOCOPhlAn version is 201901, so you are actually using the latest one. That a species has no markers in the MetaPhlAn database could be due to different factors, like we were not able to find, at least, 10 species-unique marker, or that at the time the database was created, no annotated genome of those species was present in the UniProt Proteomes portal.
I will point @fbeghini here, he was the person in charge of building this database and probably he can help you better than me through this process. In the meanwhile, you can take a look on this post opened recently in the MetaPhlAn subforum: How to create marker sequences from a genome to add to metaphlan database?
Best,
Aitor