Imagine the strain Examplomonas oldii, that is now classified as Examplomonas newii, but the old name should be kept in the correct new name. Is there a nomenclature?
Synonyms may arise whenever the same taxon is described and named more than once, independently. They may also arise when existing taxa are changed, as when two taxa are joined to become one, a species is moved to a different genus, a variety is moved to a different species, etc. Synonyms also come about when the codes of nomenclature change, so that older names are no longer acceptable.
For any taxon with a particular circumscription, position, and rank, only one scientific name is considered to be the correct one at any given time (this correct name is to be determined by applying the relevant code of nomenclature). A synonym is always the synonym of a different scientific name and cannot exist in isolation. In this case the first oldest name available or description should be the correct name.
Thank you both very much. I thought I'd seen this some time using some latin - something like 'Examplomonas newii (falsus oldii) Perez 2004' so the strain identifier is kept.
Now I also found a publication, but there not only the species classification was wrong, also the genus was falsely classified. They simply write a "formely known as" and carry both names, as you suggested.