I don't think FME has any concept of vertical datum as a dataset property.If you have ArcGIS you could define the coordinate system including the vertical CS in a shutdown script.
Hello@jecollins
I believe the CSMapReprojector may be the transformer that will solve your issue.Not only are you able to do a standard reprojection, but you are also able to set the vertical handling.The documentation for the CSMapReprojector can be found here:
https://docs.safe.com/fme/2017.0/html/FME_Desktop_Documentation/FME_Transformers/Transformers/csmapreprojector.htm
Depending on the location of your data, you may also try the GridInQuestReproject(Ireland/UK data) or the GtransReprojector(Sweden data).
Some articles that may be beneficial to providing some more information can be found here:
https://knowledge.safe.com/articles/585/using-coordinate-systems-within-fme.html
https://knowledge.safe.com/articles/29325/creating-vertical-adjustment-grid-files-for-use-wi.html
I hope that helps.