Variant subtype feature colouring lost on Get Cross-References

Fetch Ensembl gene ENSG00000123569.
Load VCF data (I used Stuart's gnomAD dataset), or load the attached exported features file via "Load Features/Annotation".
Feature Settings shows a different generated colour for each specific variant type (stop_gained, stop_lost, missense_variant etc). As it should.
Now Calculate | Get Cross-References | Uniprot for split frame view of CDS and proteins.
All variant feature colours are changed to red.