If you have strains with missing data and you want them to be reconstructed, then you must give them the value ?. For example, if you are running a reconstruction of country and you don't know the country for a particular strain, you should set country to ? in the metadata file for that strain. Then, traits will estimate the most likely country value for any strains where you have provided ?.
If you do not want these traits to be reconstructed (you would like it to remain clear that the country is unknown for this sample), then simply leave this field blank in the metadata file.
Note that each value -- empty strings, NA, unknown-- will be interpretted as a valid value! So, it's best to be consistant with whatever you use for missing values, or those with NA will be shown as different from those with unknown!